If the filename (without the folder, just the filename) of a wave file exceeds 95 characters, mIRC is not able to stop it.
Just get a wave file and rename it to be 95/96 characters to see the difference.
For example //splay path\to\<96charactershere>.wav | .timer 1 3 splay stop
The -w switch doesn't help either.

Confirmed!

mIRC v7.32, Windows 7 64-bit

Thanks for your bug report. It looks like the Windows MCI API has a filename length limit of around 100 characters. When you specify a filename length longer than that, the MCI API fails. Due to the number of issues with MCI in previous versions of Windows, a sound playing backup was implemented whereby if the MCI failed, mIRC would revert to playing the sound using a simpler API, to ensure that a sound played in case it was important to alert the user, however the simpler API has no support for controlling sounds. That is what is happening in this case.

Ok. I take it there is pretty much nothing that can be done to fix it but what about moving on with a better API?

This is already on my to-do list. Unfortunately, the alternative APIs (DirectShow et al.) have their own issues and dependencies and are more complicated to use. As the MCI method is used throughout mIRC and has been tweaked over many years to work the way it does across different versions of Windows, it would take much work, several version releases, and a lot of user testing on any new method before it will work in a way that is hopefully reliable and backward-compatible.