Strange. Sorry to hear you had that issue. We had that experience when we didn't remove the nubs, but several cars we have now done have the coils setting positively and don't move. May I make a few suggestions, since you are already far along with modifying your coils?
When we went through figuring out what was going on we were surprised a few times with what we found. I think this was, in part, because we did not realize the shaft was not parallel to the plug AND that it narrows! The nubs - we initially didn't think they were an issue, but found that the shaft narrows and its angle conspire to interfere with the coil female tip sitting on the spark plug male tip. I would suggest two simple things - first trim the rubber nubs at the bottom flush. Second make sure you have
the red tip cut like a pointer as the DIY shows. Now when you go to install it, the last little bit takes some pressure. I install them with palm pressure, until the pointer is nearly flush with the top of the shaft.
Post #5 on the thread covers most of this, if the reference helps. Thanks to
@RSL for the N54 cutaway photo, it really put a visual to what we discovered with measurements.
When fully seated it should look as
this photos shows.
Hope this helps. I assure you we were bolloxed several times while figuring it out.
Filippo