Arduino IDE: Sketch changes won't apply with subsequent upload

[glydrfreak]

In both Arduino IDE and Visual Studio, if I upload a sketch and let it run while I edit the same sketch for a while, sometimes it is as if the uploader just falls asleep.

This is what I mean:
Verbose output during the upload claims to have uploaded successfully, except none of my changes carry through with the newly uploaded sketch. The simplest way I've been able to prove this is by printing to the Serial Monitor, then commenting out the Serial.println() and the line will still be printed in the subsequent upload, even though I have it commented out.