Unexpected Behavior after using debugger

I was writing a program for my intro course and was originally debugging by hand and then after there was an error I couldn't decipher, I switched to the actually debugger and did a step-by-step run through and solved the problem. I then stopped the debugger and ran it normally and the behavior went wild. Specifically with try-excepts the IDE would skip lines and automatically enter inputs as blank and in the console multiple "input" lines were concatenated and the program was untestable and unrunnable. As it was a short 30 line program, I ran it in IDLE and it ran perfectly with all test cases. This was on my laptop.

I then switched over to my desktop for an easier work environment(and the fact even new files were experiencing unexpected behavior) so I downloaded Pycharm on there and wrote a different program. Same process as above, debugging by hand, getting sick of a single run-time error and switched to the debugger. Works like a (py)charm and I switched to normal mode and random behavior is occurring again. I ran it in IDLE with all of my test cases and it works perfectly. In Pycharm, even in debugging mode, it's jumping input statements seeming randomly. I tried invalidating cache and restarting, then creating a new file, pasting my code in there, and it still is throwing the error without running the debugger for the new file. The configuration is still default. My assumption is the debugger creates/changes some sort of project setting that I am unaware of(though not new to PyCharm, I am new to using the debugger).

Things I haven't tried yet:

-New project file

-simple input statement tests in a new file or new project

 

Thanks for any help,

-Nick

 

 EDIT:

I tested a new project file in a new window with two test inputs and a print for both variables and it worked fine. I closed it and ran the same test in a new file in the original project and it was no good. Then, I opened the test file from the new project in the same window as the original project and it resulted in the behavior. Additionally, something I just noticed is in the buggy console, the outputs(from program to console) are red and sometimes white and the inputs(user typed) are white but on the working console the outputs are always white and the inputs are green. That may be more relevant information.

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