It doesn't matter when you contracted. AFROTC wants ALL of your previous transcripts and counts ALL of the grades. So this could actually help you if you did well in those community college courses you took.
What most likely happened is that your cadre never got a transcript from those previous courses. If you didn't tell them, they wouldn't know. You can't expect them to know everything. You really need to tell them now before it becomes an issue later. I was a transfer student and had to go to the registrar and specifically make sure that AFROTC got the transcripts from my original college that said what courses I took and what grades I got. Right now, make an appointment with your cadre, and ask them if they have your previous transcripts (most likely not). Then you will have to make sure they get them, and then will enter your grades on your form 48 which will calculate your AFROTC GPA. Even if your current college does not count them as transfer credits, AFROTC counts the grades. After they receive the transcripts, they can figure out whether you have the minimum GPA for Scholarship retention.
GPA becomes a bigger factor in everything the farther along you go in AFROTC. It also becomes harder to maintain. What you really need to focus on is why you did poorly this semester - whether it was just a certain class, or certain classes in your major, whether you need to switch majors, etc.
Edit: I just saw that you had considered switching majors but decided to stick it out. Good luck! I hope you do well. As an engineering major, you can get scholarship benefits for up to 5 years if you need 5 years to complete your degree too...that may be an option if the load is just too much. Believe me, I know - I'm a Mech Eng. major taking 21+ credits a semester.