Low D "jumping" on tenor sax?

I've played Bari sax for four years and I'm being made to play tenor for marching band this year. I just got a Selmer TS500, and when I play low notes (specifically D and E) sometimes it will "jump" like it will sound as if I'm playing with another tenor and I'm horribly out of tune. Sometimes it will make constant waves, sometimes it will just do it a couple times, and sometimes it will make a solid tone. Tonguing seems to make it do it sometimes. The instrument is brand new, I've checked for leaks and cant find any. I can play Alto and Bari fine so I dont THINK it's my embouchure but I could be wrong. Anyone ever had this before or have any idea whats wrong?