I just tested playback of a local 192kHz file in Foobar with no hiccups using Lynx ASIO, while min/max MC (in tiles mode at 1920x1080).
Then I switch to playback of MC for the same file, and I can make playback hiccup every time while min/max MC (in tiles mode at 1920x1080).
This isn't a fair test.
You're asking Media Center to do work and organize its own process memory when you minimize and restore it.
This will, of course, affect Media Center and its playback more than it will effect a separate process on the system.
If you could find a 3rd party program that causes a skip in Media Center but doesn't in another player, it would be a fair test.
With regards to minimization, we do relatively heavy work on program minimization. We unload the skin, much of the database, and compact process memory.
It is a priority for Media Center to have as small of a footprint as possible when minimized.
Possibly this work could be done more gradually or even be optional. However, this isn't a widespread problem or even one we can reproduce, making it hard to know what to tune.