Thanks for posting!
This is the usual behavior when a solution is having issues with lost file references. This may be due to a server machine change during your upgrade, the fact that that the databases are now in a different location,or the databases are no longer part of the solution. Either way, there may be file references in your solution that are possibly no longer valid (the file reference path does not properly point to the particular database).
In terms of the major speed loss you have noted during launch, broken file references can directly affect performance. When a database has file references, it will look at the list of file references during launch and open the other databases. If a file reference is broken, the database will get hung up searching for the referenced database.
Let's open the 'problem' database and go to File > Define > File References. Make sure that the file references listed here are correct; I suspect that we may see some issues with references for the 50 States and CCAF Master Database files. Here, you can remove any dead references or add new ones. Note that you can also remove any file references that include an asterisk or * to increase performance time.
Let me know if there is anything else I can clarify for you.
Thank you so much for this suggestion! We're not really sure where or why those references came from. We even checked the old server that hosted filemaker before we upgraded and we couldn't find either of these files or references. Deleting them fixed the sort issue we've been having.