The original backup I made when I first rooted my phone doesn't show up with all my other backups. Is it bad that its gone? I assume i accidentally deleted it at some point. Could this cause problems in the future or should I be ok?
I'd say you should at Minimum have ONE operations backup of some ROM to fall back to... but this is a good question that I'd like to see what other say.
You can get a stock rooted version over at xda should you ever need it. I deleted my original nandroid once I saw that and try to keep a few good nandroids on file. Safer to keep it but you should be alright.
If you're like me, the chances you'd actually want to go back to that backup are pretty slim, and as SoDev pointed out, you can actually download and install rooted versions of the stock OS if you ever really did want to go back to that.