Originally Posted by mARC

What have you removed/replaced when fitting the window?

If you've replaced original undamaged parts from the original door you may need to check for damaged/bent items.

When fitting windows it is best practice to have all items that have adjustment in them loose 'read screwed in just enough as to not fall out', and the window fully extended up.

Once the window is fully extended and properly fitting in the seals check what is going on with the loose bolts i.e are some sitting higher/lower then others. This will enable you to see where the various parts of the regulator are sitting.

Focus on the areas that are not sitting flush as this will give you an indication which areas may be damaged/bent.

Are you sure the inner door panel is not bent in any way, and also check that bottom rail where the window slides into needs adjusted as this would most probably be what is throwing the window out.

It is extremely important that you never fully retract a window that you've not tested 'read doesn't freely move up and down', with the bolts tight, as this can lead to the window breaking, pieces bending to suit ill alignment.