Thanks Kevin Sjoberg for the initial response, but it turns out I have a bigger issue.
Which is if I run :set filetype? from within my Markdown file then it reports back that Vim thinks the filetype is modula2
I'm not sure how I can fix this, so if any one knows then please do comment!
As a temp fix I've used the following work around...
fun! StripTrailingWhitespace()
" don't strip on these filetypes
if &ft =~ 'modula2\|markdown'
return
endif
%s/\s\+$//e
endfun
autocmd BufWritePre * call StripTrailingWhitespace()
...so it checks for both modula2 (whatever that is?) AND markdown files.
UPDATE: well it seems this is a known issue https://github.com/tpope/vim-markdown/issues/15 so I tried the suggested fix...
au BufRead,BufNewFile *.md set syntax=markdown
...but that didn't help, Vim still interpreted the file as modular2
Also tried adding the following into my vimrc file...
au! BufNewFile,BufRead *.md setf markdown
...but that didn't work to change the format.
UPDATE 2
Fixed it, the suggestion by both https://github.com/tpope/vim-markdown/issues/15 and Kevin Sjoberg were almost there.
I just added into my vimrc file a modified version of their suggestion au Bufread,BufNewFile *.md set filetype=markdown