I've got a strange problem with python paths/eggs. When I run any tool that produces html/text output I get the error: 
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched.

So if I close galaxy, delete the eggs folder, run fetch_eggs.py (on the cluster, sourcing the same files as galaxy does so the python path should be identical) it gathers all the eggs it needs for python 2.7.

Running a job then ends with the proper results, no errors, but not with python 2.6 eggs present in the eggs folder alongside the 2.7 eggs. Re-running the same job, or running any other that produces html output, not throws up the error mentioned above. 

I can't see anywhere where I've missed a python path or anywhere where python 2.6 is mentioned. 

Any idea what I'm missing here?