I recommend you work directly with support on this one.
I found an article on the msdn forum that sounds like it might be a place to check:
The key is where the error is telling you that it can't find the file specified. There is a post here on thwack that describes rebuilding/repairing your Microsoft SQL Server Compact Edition. You can read it here: Solarwinds Job Scheduler will not start
Hit up support, I'm sure they've seen this before.
Thanks for the replies - I upgraded to veersion 10 in the end and it seems to have fixed the issue - not sure if it was the SQL SP1 install or the NPM v10 install that fixed it but it's working fine now.