Thanks for uploading your sample...
But I cannot reproduce your issue. I tried to replicate your settings as good as I could, but I got a very nice result. BatchMux had no complaints. I used the first 3 subtitle tracks, and something is wrong here. Only the first subs track shows English subs, the other 2 just show question marks. Weird...
I know almost nothing about subs, might well be that BatchMux stumbled upon one of your subtitle tracks. But it sure has nothing to do with the PAL Speedup option. At least not on my machine.
Get my test results here:
https://www.sendspace.com/file/k6ul79