It looks like you were retro-crediting rather than just letting it credit automatically. Are you sure you typed in everything correctly? Once you get one bit wrong it just won't work online and won't let you retry. The system is VERY fussy about flight number, for example, I've found that two digit Olympic flights number have to be entered as either three digit numbers in the retro claim form (OA064 instead of OA64). Could it be something as simple as that?
As for claims that are simply denied for no apparent reason - I had a similar problem a couple of years ago with an SAS flight. the middle leg of a 3 leg itinerary just wouldn't credit. I had no boarding cards but I managed to get A3 to keep pressing SAS and persistence paid off - it eventually credited about 4 months later. Crazily, the initial response from SAS was "We don't operate a flight to Krakow". They did (and it WAS mainline too) - I am absolutely 100% sure where I flew to, SAS!
Aren't boarding cards almost a thing of the past now anyway? I very rarely have one these days with OLCI. I tend to still have an electronic copy of most in my phone, but does that really prove anything? Give me 15 minutes in Photoshop and I can 'prove' to you that I was on any flight you like.