I am in the midst of a redsign, db change from PostGRES to MySQL, and upgrade from MT3.2 to MT4 --- and things are not going well.
My biggest issue so far is I have created an Entry (formerly Indivual Archive) template - when I run a site update, it updates/builds on about 1/3 of my entries the other 2/3 are ignored.
I have NO idea why this would be.
Any ideas out there?

Are there any messages appearing in your activity logs? Any indication what entry publishing croaks at?
No, there is nothing and that is what is driving me crazy - We have gone through all the logs and it simply doesn't pick up those entries. No error, no permissions problem, nothing.
Now, the oddness continues. On the Entry template, I have a small sidebar that creates a link list of entries based on a certain category - if I take this out of the template - then all the pages build. If I leave this in, then only the 1/3 of the pages build. It doesn't matter if the given entry has the desired category or not.
It is freaking me out.
I can't point you to my blog, it is behind a firewall (which does not help, but the security guys won't budge on this one).
I can paste in some of my code if that is helpful?
Could it be a problem with the DB and Categories in the MT3 - MT4 upgrade? If so, any idea what to look for and where?
Thanks JD