Memory Alert is a program that tells you various things about memory usage under Windows 3.1. This version also shows you how much low memory (< 640K) you have available. Due to a bug in Windows (both 3.0 and 3.1) when you compile apps with the -Gt flag the data is loaded into low memory. Since every app needs a little of this memory, you can run out. The "system resources" mentioned in the about box of the program manager does not take into account this lower memory. If Windows says there is insufficient resources to run an app, but you have lots of free system resources, you are probably out of lower memory. This can be confirmed with MA.
