Thank you for your post.
From your description, it is difficult to determine the cause.
Have you tried using FileMaker Pro to access a hosted file on a non-virtual server? If so, do you still have the same issue?
Have you tried a different copy of FileMaker Pro?
What other actions are being performed on the virtual server when you encounter the delay?
I'm sorry that it's such a broad bug report. I'll do my best to get more details for you, but while I've seen this frequently, it seems random for when it will be an issue. The strangest part is the high CPU usage on the server while the wait is happening. The CPU is totally maxed out while FMP is waiting, and just running the script doesn't bring up these issues.
I've seen this from many different FMPA clients on different connecting to different remote servers, virtual or physical.
I've seen this issue when there is no activity on the server (no scripts being run, backups, etc) and I'm the only connected user. FMS is the only thing installed on these machines as well, so there isn't another application taking up this CPU time. In addition, it's clear from the activity monitor that FMS is what is maxing out the CPU.
One the step-into is complete the CPU usage returns to normal, minimal levels.