First, go to home/library/application support/bowtie/ Find the Geektool.BowTie Theme and right click to show package contents. Open the .html file in a text editor and where 'Helvetica Neue LT' is, put whatever font that you'd prefer and have installed on your system. Save it and close. Double-Click the new saved BowTie theme and it should reinstall the good one. Quit BowTie and restart, Voila!
The reason yours is showing up as a different font is because you don't have Helvetica Neue LT installed.
You can download the Helvetica Neue Light font from this link for free.
If you have it opened in a text editor then save, it should let you without any problems. If so, pull the .theme out of it's file onto the desktop and show package contents there and change it there, then save it. Get info and make sure it's not locked or that you have write privileges to it and all should go as planned.