Acronis loses a timer wait issued by a program running at the same time

I have a program that is running at the same time as an Acronis backup.

At certain times throughout this program it issues a wait for up to 5 minutes at a time.

All works well until the Acronis backup completes.

If at that time my program has issued a wait then it never completes.

At present I have no choice but to not run this program whilst Acronis is backing up.

Any Suggestions?