Oh...duh! Yes, it queries the db to get the prefixes, however, other products also have their settings truncated that use other types of option code. The first product I noticed with this issue seemed to have an issue with the option code:

When I removed that, and left it blank so the simple text box shows up, then the settings weren't truncated.

Okay, I got the issue sorted. It had to do with a custom ad rotation product.

It has a function defined in a plugin hooked at "admin_options_print" that should be within the if-then construct, instead of outside of it, which causes the function to be re-declared, throwing a fatal error.