Different data area on the local machine for the users?
Or network based storage of 'local' Notes files? (In e.g. each users share on the network server 'maps' up when login on. In e.g. \\server\users\%username%\lotus\notes\data to use UNC as an example)
If it is shared, local and works for one and not the other, this is a strange issue, yes. If that is the case I am still leaning towards OS specific checking, for nothing else to eliminate it as a possible cause.
The other check you can do is to verify ACL for the user with trouble to the .NTF/.NSF databases in question...
Separate accounts, do you mean separate user id and separate mail files, I guess?
A lot of questions, but it is just an effort to narrow down the problem...
Brgds,
TrooDOS