Hi James,
Your general Mach3 settings are stored in a <your profile>.xml file.
When things go wrong with Mach3 there is generally no need to re-install everything because you will almost certainly have your last known good settings stored as a file in your xmlbackups folder. Restoring can be done manually by renaming and copying/pasting the appropriate .xml file but within Mach3 the Operator / Restore Settings tabs can do it for you (with onscreen instructions).
Hope this helps you at some time in the future.
Tweakie.