Hello Ollie,
I'd like to say that nothing is changed according to the subtitles handling in updates. I just checked the MP4+external srt with the latest release of home version (which is 6.1.1707.6, both portable and standard). And it cuts the subtitles as expected.
Before trimming, please check that the subtitles stream correctly loaded in a Video Splitter and is marked for trimming. To do that please go to the "Control"-"Select Streams" menu. The necessary stream should be checked with the white scissors mark.
Also please keep in mind that external subtitles should have the same name as the video file (except the extension, of course) to be correctly loaded in Video Splitter.