I had an issue on an earlier site build where entries containing a Matrix field with numbers of rows in excess of about 60 wouldn't save. The Matrix field in question contained two Assets fields, a couple of text fields and a PT Pill. I thought I had traced the issue to a problem in upgrading from Assets 1 to 2, and for various reasons ended up downgrading to 1 again as a solution.
I've now run into the same issue again on a brand new site, with fields exactly as described above, using Assets 2. It's for a photographic portfolio - the like of which I've built several times before using Assets 1 and never had this problem. What happens is that when I try to save the entry, when having gone above a certain number of rows, the browser load bar sticks, and eventually (after several minutes) I get an internal server error message.
There's no issue on entries with lower numbers of rows, and there's no issue with opening the entry for editing, only when saving.