Okay
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Slow remuxing - this is happening becase some videos are "corrupted" and ffmpeg is not able to copy remux them, there is not option but to slow remux them:
--> [mpegts @ 028dcc40] pts (101421) < dts (108621) in stream 2
--> av_interleaved_write_frame(): Invalid argument -
The aac_latm - I see for some reason while remuxing from ts to mkv your files are changing from aac_latm to aac_adpcm. I don't have any sample file that do that, all my aac_latm are preserved. However I will try to get to the root of this. Can you upload one sample file with this issue and post back when done. (small one about 300 mb)