Your images are too large for me to view, my internet pipe is too small, but others may be able to compare them better, so stay tuned.
Anyway, yes, you can sometimes get noise in an IR spec, caused by CO2 in the atmosphere, or adsorbed onto the plates. The IR spec experts at work would occasionally flush the chamber, or the KBr plates, with dry nitrogen from a clean tank, to get a better scan. You can certainly try it, and see if it improves the scan.
Of course, one instrument or another could be slight out of calibration, or have slightly older optics or electronics.