I've been planning to throw some time at Indesign after the holidays - I'll try a big-honking font embedding test then (I've got fontfolio8 and fontfolio11 to try). I've had spotty hits and misses so far with font embedding - sometimes open types work better than truetypes, sometimes not. I think it has to do with the licensing embedded in the individual fonts, and I just haven't worked out the specifics of how it works.
Having Microsoft's font Properties Extension
http://www.microsoft.com/typography/...roperty21.mspx helps discern things - until you hit a type 1 font. Doesn't offer so much info on those. (Are you using a Mac or aPC - I've forgotten).
I've run across some weird output formatting in Calibre, too - carriage returns and style changes that are not in the source, etc. I haven't been able to replicate it yet, so I'm not sure what I'm looking at.
Maybe the real questions are about 2-fold problems:
1) Problems specific to the epub reading software
2) Problems specific to the epub generation software.
I'm finding that problematic epubs behave very differently in different reading softwares. I can't get fpreader to run at all on my computer anymore, the reader for opera won't open anything I can throw at it, calibre's won't open output from indesign, and DE is just plain weird - chapter headings need to be really short, or the TOC doesn't work right, for example.
For being a "standard", the implementations (of both generation and reading softwares) seem to be catering to specific developer's stances, and universality is still a ways away.
Reminds me of Java.
-bjc
P.S., oh, uh, things to try:
I've found that editing in Indesign is hit-or-miss in the output. Seems that the source all pretty much needs to be perfected before importing into ID4 - you should be able to copy and paste your bad chapter back into word, and then re-export it as text, html, and doc's to see if anything shows up as weird. Tweak in Word, Then reimport from the word doc back into ID4.
Hope that helps.