Big Boy starts immediately upon Cab-2 power on

Check to see if the IR link between the tender and locomotive is good.  I've had the tender come up in conventional and the locomotive in command.

power the legacy cab 2 and base first. then power the track.

Well, if all the smoke units are enabled, the BB will suck up over four amps, you may need more transformer for one thing.  When I fire up the VL-BB and blow the horn, I'm at about 4 amps.  If I'm pulling a large consist, I'm sometimes hitting 5 amps.  The BB is a power hog, nature of the beast.

We need more detailed symptoms.  Does the locomotive still run in command mode?  Can you open the coupler on the tender from the remote after powering up?  Does the reverse light on the tender come on when you change directions?  If neither of these work, I agree with sinclair, the IR link is suspect.

Yes, that is the weird thing, everything works as it should, and if I turn the brick on first and then the Cab-2, it works correctly.  Cab-2 powers up, I enter the train or engine number for the BB, hold down the power up button, the dialogue begins as it should and everything is OK.  Tender lights up when put into reverse. I hear all of the stereo sounds coming from it.  Couplers open fine.  IR looks ok, but its just latch, not sure what else to look for. I don't think its power related, but will add one just in case.  I've now added the water tender and 3 sets (of 3) refer cars, one has the freight sound and it pulls perfectly fine, sounds are great.

My only problem is that I must turn on the track power first, then the cab unit if I want to initiate the power up sequence.  I guess thats not the worst problem to have, but its still aggravating to me none the less.

One thing I did not mention was that this began happening after I was messing with the LSU where at one point I went back to normal operation and forgot to pull the cable out of the computer and the base unit.  It does act strangely like you would expect if you were running in conventional or lost your data cable connection from the base.  If it didn't happen on a completely different layout with a different command system and wiring, I would suspect a problem with the base unit or shoddy wires.

I can't even imagine what is going on.  If you power up without the base, after a few seconds, you should drop into conventional operation, not the other way around.  FWIW, my VL-BB acts as I would expect powering up before or after the command base.  I actually turn the command base on with the power, they're on the same switch unless that track is turned off.

How many TMCC/Legacy bases do you have powered up at once?

Just one base at a time.  With the other one powered off and disconnected from its perspective track.  The problem is really unique.  When I apply power to the Cab-2 (Base is on, loco lights are on, everything is quiet) it begins the power up sequence.  Still the Cab-2 presents the power up/down screen.  I press power up (#7), and the only thing that changes is the screen, as you would expect, it goes to the normal screen where I can initiate all legacy commands normally.

Its not going into conventional mode, or at least I don't think it is.  I wonder if Lionel has a secret super decoder reset sequence that reloads the firmware.  The one in the manual is just an engine ID reprogram and it happens way to fast to be reseting the logic in the BB.

What you describe sounds like the CAB2 is sending out a command, possibly a stuck key?

the only way conventional mode would work, would be if no legacy/tmcc base is plugged in.

Both Cab-2's would have to have stuck keys.  I put another locomotive on the both main layout and test track and it starts normally.  I think I've tried just about everything, so I'll be talking to Lionel tomorrow.  Its such a small thing, but if I ever decide to sell it.....

Lionel told me that the Big Boy is the only loco that will start up on its own if the brake slider is not completely off.

That was it!  Leave it to me to find the rare oddity.  They don't mention this in the manual anywhere (at least as far as I could find).  Wow, thank you!

 You don't have an oddity. All the Big Boys will do that (vl)(early 990 systems). Mine did this and I thought something was wrong as well. I sent my 990 system back 2 times before Lionel sent a whole new 990 system. The very friendly Lionel tech called me and we talked for 20 minutes. This Big boy startup was only one issue of a few others I had.  I took the time to send in a video I made to show all my issues. The tech picked up on the location of my brake slider on the cab 2from the video and was able to tell me about this premature startup. The Big Boy is the only loco to date that does this and He also told me it is not in the manual. While Lionel had the 990, I asked them to upgrade it, so he installed the latest version in the new 990 system they sent to me. I will have to check, but I believe the startup no longer occurs. Glad I could help. I cant believe this hasn't surfaced somewhere before now.