Have you checked the vendor history to see if there is really that reference number already posted to that vendor?  For example, posting the reference number Feb two years in a row will cause this problem.

I believe this message stemmed from a bug that has been in the program for over a decade.  If more than one entry has the same number, the program cannot lookup the entry properly and show you the data entry screen when you double click it in the Vendor History.  So they probably put in this message to make sure people post with a different one.

I haven't tested this part of the program in years so I don't know if they still have problems with this area.

Yes.  I've even changed the reference number to something that I know is unused and it still doesn't work.  What bugs me is that it works fine in single-user mode.  Nobody else is posting payments, so I know it's not a matter of refreshing data.

It may be reading data from before 2014 and seeing a duplicate from a prior version that didn't check, then panicking.  That code may not run in single-user mode because it couldn't possibly find a duplicate.

If the problem is consistently with a particular vendor or vendors, you could close off the vendor record and start new.

Or restore a test file, and see whether the more drastic step of purging older data will remove the problem. 

You could also try Sage support.  My past experience has been that they suggest clunky, impractical work-arounds exactly like the one you've already found - they suggested switching to single-user mode to enter vendor credit notes. 

(While the other dozen users take a long coffee break?)