how does quartus decide to remove logic?

If you have logic/memory that has no connection to pins, or no reason to connect to pins, then there is your problem. are you making a write-only memory?

You need to buy one of these: http://www.national.com/rap/files/datasheet.pdf

Basically, it sounds like something is not connected. Just because you have memories that load counters wont be the problem. aslong as these counters address some memory, then eventually has an output that goes to a pin, then fine.The memory doesn not need to directly connect to a pin.