There is a problem with syntax hightlighting using "Shell Script (Bash)". The following reproduces the error:
MESSAGE="$((module load mymodule) 2>&1)"
echo "This is always highlighted yellow now, as if it is part of a string"
It seems like the second close paren does not close the $(...). Everything under the "MESSAGE" line no longer has correct syntax highlighting in SublimeText. This is working bash code.