Only time I have seen something like this is when someone is mining LTC.  Seems to be pushing those cards to do more memory based things versus GPU based things really is havoc on those cards.

I read through the OP as well as his responses, and I am not seeing any place where he said he was concerned with lag.  He just said he wants to be able to control it.  Maybe I missed it....

If he isnt worried about lag then a free solution like TV would be better than dropping money on a wireless KVM.

Take our the "name" lines in your config file.  Make the first two pools look like the third one you listed.

What ASIC miners are you referring to? Or are you referring to FPGA/Block Erupters?

If you are using a post 3.1.1 version of cgminer then you need to use zadig to change over the USB association for your devices from FTDI to winusb in order for cgminer to recognize them and run.  All information can be found in the README's that come with cgminer.

I have both Windows machines and BAMT machines, easiest solution is Putty for your BAMT units, and Teamviewer for your Windows box.  There is an iPhone (and I assume Android version) of Teamviewer that you can use to control your Windows box with, even on the go.  And for your BAMT boxes, install Putty on your Windows box as well, Teamviewer into it from anywhere, and then putty into BAMT from there.  I do it all the time without a hitch.  Heck, I even have an SSH app on my iPhone that when I am at home I dont even need to go into Windows to access my BAMT units, just do it right from my phone (I have them set to static IP's of course).

Because that chart is for BTC, not LTC.  Different settings. 

Yeah, change your intensity to 17, your worksize to 256, your memclock to 1180, and your thread concurrency to 5760

If you are mining LTC, then you need to increase your intensity (go back to 19) and also mess around with your memclock and thread concurrency.  Try adding these.

-o http://yourpoolofchoise -u username -p password --auto-gpu --auto-fan --gpu-engine 850-1000 --gpu-fan 0-90 --gpu-memclock 1180 --temp-target 75 --temp-overheat 95 -I 17 --thread-concurrency 5760 -w 256

Sure post it.  I didnt catch it at first because the settings you listed before are for BTC mining, and if you are stating kh/s then you are scrypt mining LTC, right?  Those are different settings.

Some of it is for backup purposes so if a pool goes down, they are not losing time mining.  Some people want to split their mining to get better "luck" if they are using DGM to calculate their earnings vs PPS.  If a pool gets stuck with an unfortunately long round then they are getting less out of it so this allows them to cut that loss down.

In the end PPS and DGM are going to yield about the same results in the long run.  DGM has the chance of getting lucky and getting better payouts quicker, but also you take the risk of getting unlucky as well, where PPS is steady and constant. 

I personally use PPS because I like the consistency and being able to predict what I am going to get without any surprises (except for network difficulty increases).  I have backup pools setup in case my main pool goes down so that I am not losing mining time.

I think this was answered on the cgminer official thread by ckolivas.  You need to update your SDK, 2.1 doesnt work with scrypt.

First and foremost, install catalyst drivers 11.12. If you have higher, use driver sweeper to clear out your current version, and then install 11.12.

Secondly, run this line.

-o http://yourpoolofchoise -u username -p password --auto-gpu --auto-fan --gpu-engine 850-1000 --gpu-fan 0-90 --gpu-memclock 600 --temp-target 75 --temp-overheat 95 -I 12

Try that and see what you come up with.

Have you tried getting a replacement from BFL?  When I got my Jalapeno, it didnt come with a USB cable like it should have, so I had to get my own.  I told them about it and they sent me a cable still.  I know there was a user who reported one of his fan blades broke on his Jalapeno and he requested a replacement from BFL and they sent him one.  If you only had it a few days and the power supply indeed was faulty and burnt out, they should send you a replacement.

Jalapenos, and anything that comes from BFL are pre-configured to work with Eclipse, because Josh from BFL, owns Eclipse and of course they would prefer you to mine there.  Doesnt mean it was being used there.  They want you to use their products on their pools, no different than any other company.

bfg/your miner requests work from your pool to do, then submits its work and asks for more. From what I can see, your pool is slow at delegating work to your miner, and even when it does its small shares so your miner is sitting idle more often than it is actually mining.  Maybe you should try a different pool.

The reason I asked about solo mining is your api-allow argument is for a local machine and usually I only see that if someone is solo mining. 

When it comes down to it, I dont know/think there is a way to get it to connect and load all settings if you are not logged in. When you log into an account, certain windows files are unlocked and made available depending on the user privileges (administrator, guest, etc).  And I think that is what may be causing you to not be able to get all of our settings to work.  But I could be wrong. Sorry to say, if you cannot have this system ran with no password and a single user so that it loads the desktop once turned on, I dont know if you are going to be able to accomplish what you are looking for.

You hit on your problem earlier and didnt even realize it.  Sad to say, but if you want to run 5xxx cards you will need to roll back to a version of Linux that will support 11.12 drivers.  Any drivers above that are junk for 5xxx cards and you will lose performance.  That is the reason why BAMT ran fine with 5xxx cards, even after updating cgminer, the SDK and drivers remained the same and you got optimal performance.  The only reason to update the SDK and drivers beyond 11.12 is if you have 6xxx or 7xxx cards that you need to get supported and mining.

I am running a 5870 and 5830 in a BAMT box with cgminer 3.1.1 and with OC'ing I am getting 430+ out of my 5870 and 300+ out of my 5830. 

I used to have them running in Windows and running 12.6 drivers and I lost about 20% or more performance.  Did a driver sweep, installed 11.12, and my hash rate went up.

Use driver sweeper to make sure you didnt miss anything when uninstalling 11.1 and try again.

Oh come on its fun.  Can gain another Gh/s out of each.

You might also try a UPS to help regulate that power as well.  If it is a power issue this could solve that problem for you.