The time the issue started is not totally clear yet, but it could very well have been at the upgrade from 4.3 to 4.4.
A while back I posted the following about the same client. Never figured it out and didn't think it has impacted anything except file record count. I don't know if it could have some bearing.
While inspecting a client's IM_PeriodPostingHistory file for a blank warehouse code issue, I noticed the Data Conversion from 4.3 to 4.4 had created an empty beginning balance record in fiscal period 01 for every fiscal year up to 2094 for every item in all warehouses including the blank one. GL and IM setup seem clean and I have no idea why it decided to stop at 2094.