text editor keeps adding .txt

Tried to save a perl file in Notepad, Wordpad AND Textpad. After opening a s
cript that works and saving it with a new name (with .pl extension). There's
 a slew of choices in the various dropdowns. Some add .txt., which I also tr
ied simply renaming the file (deleting the .txt), but that did not work eith
er. 

background:
The perl script powers an online calculator. We originally outsourced the pr
oject and everything worked fine. Since then, we've made some updates to the
 graphics on the website. A java script opens up a pop-up window to start th
e calculator. The calculator allows the user to enter in variables and sends
 them to a webpage that show them how using our product will save them money
. That end webpage is coded IN the perl script. 

note - I am uploading the file as asci (not binary) using FTP Pro.

When I save another .pl file and upload, the pop-up says that it cannot find
 the file. However, the original file works. 

The Going Theory:
In the proccess of saving the file, I am converting the file to the wrong fo
rmat.