Well I've already gotten rid of 07, so I can't specifically look it up for you, but I can tell you that I wouldn't be at all surprised if there was no way to solve your problem. NBA Live 07 is pretty buggy and not very friendly to customization.
At least in old versions, it wouldn't mess with the way you had your lineup unless you made a trade/signing/etc.
I might as well ask the obvious... did you put the players you want as the starters on 100% on the start slider? Since there isn't a reorder roster anymore, that's the way to do it.
I know this probably wasn't exactly helpful... but... yeah. I'm chatty. Hopefully someone will be able to crack this for you.