The "it's just different" argument is, in fact, the main reason for me. Tk GUIs don't look and behave like a native application, which affects the "look & feel" in multiple small ways, which make a complex app feel weird and clunky compared to native apps on given system.
File dialogs may be a perfect example of what I am writing about: they may not be "worse" or "better" than native dialogs on some system, but they are DIFFERENT, they behave differently to all the rest of applications on the system.
If you're MacOS X user, you may get a feel of it by comparing native Mac apps with apps running on Mac with X11 compatibility layer (like Gimp or Inkscape). They behave differently to all other apps (no menu at top bar, cmd+tab works a bit differently, cmd+backtick works much differently), so - while their behaviour is fine on Linux X11 desktop - the same behaviour feels weird and clunky on Mac.
Downside of Tk is that these GUIs aren't actually native anywhere.
For a portable UI, I may recommend wxWidgets, which are just a common API layer (a facade) for whatever native UI your system provides. It may be a bit offtopic for your current situation, but it may be worth looking at anyway.