Hey there,
This is my first post. Yaaay!
I had a similar problem today. I just finished running a super awesome mission on 100% realism, and I was all excited to get back to the sub base. Sure enough, I have to go from Japan to Hawaii on 1/3 tank of gas and I can't make it. I also can't make it to that southern port, not on 1/3 speed, not on 2/3, not on standard.
I did however make it by running on 1/3 power submerged until my batteries ran out, surfacing (still 1/3 speed) until the batteries charge then down, up, down, etc. until I made it. It took forever.
THis might be a dumb answer; I just figured it out, I'm sure you already knew.