...affected FIDs cover a large range from 336 to 69776...

That's a lot of FIDs. Do you have a lot of small files?

I know that your error distribution seems random, but I am wondering if the player software somehow reacts badly when trying to update dynamic data of a FID that is too high or references an invalid block in the dynamic partition.

An interesting test might be to reset your counts to zero (perhaps you can copy the data temporarily using dd to a file on a different partition) and try playing a series of low numbered FIDs. Check to see if it is updating. Then play one very high numbered FID and then a sequence of low ones again. This would check to see if a high FID is blocking future dynamic data updates.