Your Reaper issue is strange. I have no experience with Reaper but it sounds like your intensity (known as aggression in Reaper?) may be set too low. Another thing that can cause your problem is too high of CPU load. Since the work that the GPU does is fed to it by the CPU, if your CPU is being overworked (verifying the Bitcoin blockchain, encoding video, etc) it can cause your GPU to become under-utilized. Usually setting the priority of cgminer or Reaper to high in Windows fixes this (Ctrl-shift-esc, processes tab, right-click reaper/cgminer.exe).
As to your question about shares, you're right; the higher the difficulty of the shares that the pool gives you, the longer it will take to work on them. Thus, you'll submit roughly half as many shares if the difficulty of the shares doubles. As you already deduced, a pool will consider a higher difficulty share to be worth more and so in theory you should ultimately receive the same amount of coins whether you mine at a low pool difficulty or a higher one.
That said, you want to find a good middle ground in share difficulty. If your difficulty is set too low, you spend too much time and bandwidth communicating with the pool server and potential worktime is lost. If your share difficulty is too high, it takes you too long to solve shares and results in work being lost if the current block is solved while you're in the middle of working on a share for it. The share difficulty is set poolside so you may or may not be able to change it. Some pools allow you to set your difficulty directly (i.e. on the "workers" page of their web interface), others automatically adjust your difficulty based on the rate at which you submit shares and still others simply use a one-size-fits-all single difficulty.
I would stick with cgminer if you're comfortable using it. It's kept up to date and has a lot more features. 30-90 seconds per share sounds a bit long so I'd see if your pool allows you to lower your share difficulty.
Good luck!
