It's not you - exactly the same is happening with me; Roku 3 and Yamaha RX-V677.
I have always, always been able to decode DD+ 5.1 titles on Prime Video but lately, it's a bit more hit and miss.
The Grand Tour as an example;
Season 1: all episodes are detected as being encoded with DD+ 5.1.
Season 2: Episodes 1-8 are DD+, 9-11 are PCM 2.0.
Can anyone verify this?
Amazon have obviously changed the encoding somehow. I've had the most infuriating conversation with an Amazon 'support' person but finding someone who understood what "audio" was, never mind Dolby Digital or PCM was a challenge so I gave up.