And in the end it just sounds like it makes a better bass line. does this ever happen to any body here?
Current Gear:

Epiphone Special II
Squier Champ 15W
Digitech RP90
2 Crappy No-Name Acoustics

I find that happens when I write really simple stuff. I guess the best way out of it is to listen to a wider variety of stuff..maybe jazz or something. That way you will end up writing more interesting riffs intead of stuff that sounds predictable.....like Opeth do.