Also having this same problem with some older MKV recordings in TVHeadend where the record started before the flick to AAC 5.1.
Can't find any way of decoding them/fixing the metadata so the audio gets decoded properly in VLC etc.
Although, by accident, I've found that in Windows 10 - Windows Media Player and the Films & TV apps will both play these files absolutely fine, with no glitch on the change from 2.0 to 5.1. Microsoft's AAC decoder obviously copes fine with the AAC LATM streams in the MKV container. It'd be good if there was a way to use the Microsoft codec to decode the files and re-encode maybe to AC3.
I also had a transport stream file I recorded from Freeview HD using VLC back in 2013, the 5.1 audio in this is also broken and no amount of transcoding in FFMPEG seems to fix this (even though it's TS not MKV). This also plays properly in the two Windows 10 apps after it's been remuxed to MKV without re-encoding the audio or video using FFMPEG, so the relevant AAC data must be there in the stream still somewhere that Microsoft AAC can interpret properly. The original TS file doesn't work in the Windows apps though bizarrely! (The stereo parts at the start and end will play, but the 5.1 of the programme is silent).