Mary,
The fact that you and the user have different roles does lead to a possibility the effective rights of the user have somehow become insufficient for creating links (assuming by "links" you refer to shortcuts, not link groups). Based upon your answers I am not convinced this is the problem as long as nothing has changed for reasonable time.
It sounds like you have already done this, but could you confirm these two things:
1. The user effective rights will allow them to copy the entry from each location
2. The Scope of the rights applies sufficiently for the folder, subfolders, and documents within each location for source documents?
3. Could you tell me if there any additional users fulfilling similar roles that see the same behavior?
Your most recent post refers to higher than normal activity. Plausible, but I am not certain this would be a root cause unless more users are experiencing problems. However, you did mention in your original post noticing this behavior with prior versions of Laserfiche. This does get my attention as a potential performance related issue.
Do you have any work (such as indexing documents) that can be scheduled for off-peak hours?
If you would like to test performance then Windows Performance Monitor can be used to collect data for review. Use this link for more information.