It should - I had just recently uploaded a new version when they reorganized some CSS for no apparent reason.
Check if it's applying to the right column (snippet on the bottom of the script) and stuff?
Tried my best but no luck still (not hugely familiar with JS).
The itch script doesn't seem to have updated in over a year?
2019+ note: Userscript downloads from itch now work correctly so you should use the regular download. The link in this reply points to an older version, which is not up to date.
itch page simply links to the hosted version:
(because it's not possible to have the browser bring up the install dialog when downloading from itch)
As per tweaking, it's just changing the number in "tdf_bind" call on the bottom of the script to match the number of tweetdeck column that you have notifications in. I'm meaning to do some actual UI for this stuff, but hacking in menus on top of tweetdeck's already-unusual layout is not very fun at all.