That's easy: because the calls to the screen went through the terminal handling code; on MSDOS, for speed, many applications bypassed the MSDOS I/O and called the video hardware directly; this made things much less portable.

There were many MSDOS but not 100% IBM PC compatible machines made that got hit in the market because of this, such as the Zenith Z-100/Z-120 , TI PC, etc. If the memory map and everything else didn't exactly match the IBM BIOS setup the application would fail.