Do you have any external drives connected? Certain external hard drives will go into some sort of dormant mode when they haven't been used in a while, and will block things until they spin back up. This is triggered by anything requiring filesystem access, whether you're trying to access those drives or not.
If this is your issue, it'll be very intermittent, and caused by other attempts to access the file system (Open File and Save File dialogs being common). Furthermore, it won't be limited to just Textmate, but your usage patterns may mean it mostly shows up there.
The solution, in this case, would be to unplug the external drives when not in use.
Of course, this isn't to say this /is/ your issue, but it would more or less fix your symptoms.