Well, I wasn't able to 'fix' the issue with the pool (but will be looking into that longer term as no point having miners with difficulties higher than a coins difficulty), there was basically too much hash power being provided vs the difficulty of the coin. I  increased the rate at which the pool finds blocks dramatically so the difficulty will increases the payouts will become 'Normal'.

My apologies to everyone negatively impacted by this, but the issue is really with the difficulty being so low.

EDIT:

Basically, with difficulty being too low the pool was not accepting all the hash power being given to it, a fair % was being 'thrown away' otherwise it would have basically caused the pool to be ddos'd by miners, the pool and the coin daemon itself would not have been able to handle the load either without being on a supercomputer or something.
Miners were all being paid for the % of work overall that was not being 'thrown away', so in example above where user got 0.3 coins after finding 20 blocks (which should have been around 1000 coins) that is due to the pool overall was only accepting 0.03% of work.

Now that the difficulty is reaching a 'sane' level compared to the hash power being provided to the coin the pool is accepting more valid work and running normally.

ccminer alexis edition is the best performing miner for c11 algo. Please see page 14 in this thread. There you will find everything you need.