you've found a visual representation of the single biggest problem in FPSC.
This happens in all versions in different places with everybody, its the reason for the frame rate issues.
FPSC, a lot of the time, doesn't know when to show and hide chunks of the level...a lot of the times it shows whats unnecessary, but you cant see it (unless your in wire frame view).
Rarely though, FPSC does the opposite, and makes a part of the visible level dissipate... this has happened many times to me, in just about every version of FPSC including the current beta.
My suggestion to you, would be to upgrade, if the problem persists, email lee with a reproducible FPM...and we have a chance of it getting toned down a bit, otherwise, ive always rebuilt the parts of the level that do that a bit differently.
http://www.fpsc.seqoiagames.com