Thank you for taking the time for a detailed reply.

It did not touch upon or solve my actual issue, but I found a solution on my own.

There were possible formatting issues in the original .csv file. Even after changing the formatting of the Amount column from red text to showing negative number, QBO did not recognize them as negative numbers. 

So, being that the file was not overly large I created a new file from scratch and manually copied each transaction over. Finally, that did the trick. Still do not know why QBO had such an issue with the original, but this will not be a palatable fix for future identical issues.