Altera has made classic timing analyzer obsolete. TimeQuest is what they only recommend now. If you only have the sopc system in your design and don't need special constraints on external i/o, migrating to TQ shouldn't be difficult: simply follow instructions in the TQ tutorial.
If you want to keep on with classic analyzer then, yes, the advisor could help a little, at least with setting the correct compilation options.
Anyway, IMHO the required pulse width about 20ns means that you have somewhere in the design a 25MHz or 50MHz clock besides your main 100MHz; maybe a generated signal inadvertently used to clock something?
Cris