That is really strange, I didn't think it was possible with recent firmware for the publisher to prevent the font size being changed. I haven't seen any book that can prevent it, and I can't find any way to prevent it myself.
Perhaps you could try loading a known-good* ePub, just to make sure it is not something wrong with your device. You could try
this one from Baen's Free Library for example.
If it is a problem with the books, are any of them free? If so could you post a link to one? I'd be interested to know how the publisher has managed to do it.
Edit: For things other than font size, such as line spacing, justification, etc. the publisher generally does have the power to override the device settings if they choose to. If they have done that, then there are some ways to fix it either by patching the firmware or by re-converting the book in Calibre to strip styles completely (but Calibre can also be the cause of some of the problems, so don't do this unless you really need to), but both of these methods are blunt instruments and have side effects that can spoil other parts of the book's layout. The only way to fix the problems without causing side effects is to manually edit the book and selectively remove just the specific styles that are causing the problems and leaving the others in place.
* Edit: Known-good as far as being able to change the font size that is, it might well have other problems.