Hi,
Lately I have been experiencing the same issue, I have found though that if you select in the fmgs Position > Time and you insert the utc difference for your arrival, than you get the correct ETA updated in the F-PLN page.
The problem comes when you exit the Position page, the ETA will start again to come back minute by minute (at least in my case). If you select back the position page, the eta once again will be updated showing correct values.
Hope this helps the community and the developers to fix this issue.