If I was a betting man, I would think that this is the issue at hand, where your install, installs py 2.6.2, and needs that and is locked to that version number, but if I have py 2.6.4, it will not override what I have, so yes this is a limitation for sure. I just duped on this machine, installed py 2.6.4, then ArcMap with ESRI py, now I get two copies,, so which one do I use, in one corner I have access to py from ESRI, and in the other corner I have access to python from the user community, I suppose next up will be to ensure that my eggs are placed as part of the py26 directory, hopefully, and not the py26\GIS94 directory. Any workarounds on this without destroying our 26 updates.
Perhaps, if your install finds a 2.6.1 version, it can go ahead and upgrade to 2.6.2. If It finds anything above 2.6.2, then lets you know that there are two copies of python on your machine.