What's the difference in meaning between these two spellings when used at the end of a sentence? I get that the pronunciation is subtly different. Is there a semantic difference? 

There's a difference in register between the rising tone version and the high tone version, but they mean the same thing. Essentially, the high tone version is used in everyday speech and rising tone version is used in (very) careful speech.

 

This difference doesn't quite map onto the spelling difference though, because although the ไหม spelling does indicate a rising tone, it's often read with a high tone. It's the same with เขา, which is sometimes written เค้า but can be read with a high tone even when written เขา.

 

When reading this type of word, I find it extremely difficult to know whether the spelling is supposed to indicate the tone. Sometimes the same document will use both, which ought to make it easy, but I've certainly seen manga that use ชั้น in some places and ฉัน in others, with no obvious difference in the level of formality or the status of the protagonists. Therefore, I think there's probably more to it than the careful/casual thing. It could well be to do with stress and prosody but I haven't figured out what just what yet. If you have examples of ไหม and มั้ย in the same document it'd be interesting to see them.

(1) There is no difference in the meanings.

 

(2) The pronunciation is identical:  high tone.  (Except in highly unusual situations such as when dictating text.)

 

(3) มั้ย is typically used when representing speech since it reflects the actual tone of the spoken word.  So, for example, you'll find it in movie subtitles and in cartoon books.  ไหม is the officially correct form and is used in "normal" writing.