Max 5 elephant, big patch problem

This is unfortunatley one of those "big patch" problems that I haven't got a concise version to present for analysis. The problem I'm having is that I load up this big patch and use lots of named matrices to route my signal. So, a matrix named "alphawhite" is created somewhere and banged somewhere else to output. This all works fine the first time I load the patch. But, in a case as simple as loading the patch, closing the patch, and loading the patch again, I'm getting very weird behavior. I'm getting complaints of matrixes not "matching" the input type, and I'm getting visual weirdness where I can see that a stream of video is subjectively the wrong color... planes are being rotated?
If I shut down Max completely, Restart Max, and then reload the patch, it starts up fine.

So, my theory is that something is carrying over within Max that is messing things up. Possible offenders could be object naming in terms of scripting, or matrix naming. I've tested this without my GL layer, so it doesn't have anything to do with the graphics card/texture memory.

I'll try and come up with a test case, because this seems to be too consistent to be just an example of max breaking "under duress" from a large patch.