What version are you on?
Do a quick test.
Drag the clip from the bin to the sequence icon, so you have a sequence with the exact settings of the clip.
Create an opacity mask in this new sequence, and check if it's also offsetting.
There was a mistake on my half, the sequence and clip setttings were not the same!
But still same offset error.
Are you applying the mask directly on the clip, with no other effects?
Also try to nest the clip, and apply the opacity mask on the nest, see if it helps.
Thanks Sami, I actually followed your first instruction better, I created a new sequence again, by right clicking, new sequence from clip.
I had the wrong sequence settings, Sorry, and Thanks for your help.