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Hi,
I worked for months with Quartus II and a Cyclone II device without getting big trouble. But since a few weeks I'm working on a new part of the design and I can't get this thing stable. I use modules I wrote long time ago an that worked well so far. But now, combinded with new modules (or slightly modified old ones) they do weird things - in simulation and on the hardware. The new design parts work well without the old ones (in simulation). The problem appears only in combination.
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After creating a new wrapper design with some previously verified blocks, and some new unverified blocks, make sure this works correctly in functional simulation. Given the description, I tend to think that even though your blocks are working well in isolation, when interfaced together, there are some issues that are causing functional problems.
Changing settings in Quartus II (or in any other EDA tool for that matter) can help you only in implementation, but functionally the design has to be correct to start with.