I'm sorry your documents are experiencing probloems with the new metrics.
We found that there was a problem in the values APP used to calculate the widths of text using TrueType and OpenType fonts. The problem was serious enough for some customers to raise their support call to the highest level. The problem had the affect of making some content format very badly with the new PDFlib library. We have solved the problem by telling APP to use the correct units per em value built into the current font rather than assuming a value, which means APP is more accurate than before. This, then, has had the knock-on affect of making all documents format differently.
We're constantly striving to improve our products but we felt that this problem was serious enough to warrant a change although we knew it might cause problems such as yours.