I'm afraid I didn't put together a minimal sample, since I couldn't even get it to behave the same for both structure types. I reproduced this behavior on both the 9-16-14 and 1-17-15 nightly C::B releases. "Enable watch script" was enabled, but when I disable it and debug my program again, the watches display correctly, so I guess it's a problem with that feature? The tooltip mentions not to use it with a Python-enabled GDB, but I don't know how to tell if I have such a version of GDB installed. GDB's help output gives the following:
GNU gdb (GDB) 7.5
...
This GDB was configured as "i686-pc-mingw32".
This GDB version is kind of old, but I'd rather not risk breaking something that's otherwise working just fine if I can avoid it.