Keep getting weird tones while recording

"I am recording Mono ~16 bits ~ 44.1kHz on my soundcard and the same levels in my software. I know my software is outdated too (Cool Edit Pro)

Output filter? Like a ground loop eliminator?"  - Amethyste

A transformer type ground loop eliminator would likely be the first thing I'd try.  They're inexpensive, available everywhere, and might help you in other recording scenarios.  I've got one mounted in a plastic project case with a bunch of different I/O jacks peppering the sides.  Really attenuates serial port noise and the like.

Cool Edit Pro (THE best sharware evar) was bought by Adobe and relabled / retooled into Audition.  Adobe charges great gobs of money for it - the latest version actually guts much of the basic functionality that I use all the time for analysis, like the spectral pan and phase views.  Anyway, you might try recording to 44.1kHz 32 bit float and then dithering down to 16 bits once you're done manipulating the track (normalizing, filtering, etc.) if Cool Edit has this option (I can't remember, though Audition does).  Higher sampling rates like 96kHz and 192kHz might also be options if your hardware and software support it.  Cool Edit can probably downsample the sample rate to 44.1kHz and dither the float to 16 bits.  At any rate, try to get the lowest noise floor you can (the ground loop eliminator might help for that) along with the hottest signal you can without clipping.  You can maybe watch the VU meters in Cool Edit to see these things.

Yes, CEP has 32 bit float option!

so after I am done recording in 32 bits, I can dre-save to 16 bits and you think it might take care of the issues?

Thank you for the explanation. i have ordered a ground loop eliminator from amazon. I'll try your latest suggestion tonight and see how it goes ~ and let you know.

I totally appreciate your time!

"so after I am done recording in 32 bits, I can dre-save to 16 bits and you think it might take care of the issues?"

If you are manipulating the file at all, even adjusting the volume of the track, float can help because otherwise you're working with 16 bit integers.  Try recording hotter to increase your SNR.  In my experience having limited SNR and then boosting the level can easily lead to a non-white noise floor and other issues.  Recording at 96kHz or 192kHz might help with the aliasing, particularly if the bulk of the ultrasonic energy falls in the pass band where it could then be filtered out digitally.  Aliasing is a bear because it's a non-linear form of distortion, and therefore impossible to completely remove after the fact.

I should also add that I've experienced soundcards aliasing when strong high frequency content is fed to them, even in the D/A direction!  Make a 10 second 2kHz - 20kHz logarithmic sine sweep in Cool Edit and listen to the result, if near the end you hear a ghost tone steadily dropping in frequency that's aliasing (not amore).