So I had my bonus set to go into traditional, on the thinking that it is taxable, so I should be contributing as much tax free pay as possible to the Roth.
You're a trailblazer.
On one hand, it makes sense to put as much tax-free pay in the Roth as possible. On the other hand, your taxable pay is now so low that it's quite possible for you to pay no taxes at all. This is especially true after tax credits (Earned Income Tax Credit at lower pay scales, plus Childcare Tax Credits or other programs). Even if you're paying "some" taxes, it's still at an extremely low rate.
When there are no longer taxes to pay (or defer), then the issue becomes stuffing the money anywhere you can enjoy low expense ratios and tax-free gains. The traditional TSP funds are taxed on withdrawal, true, but in this case your traditional TSP contributions are untaxed (because CZTE) and only the profits are taxed. TSP RMDs would be taxed proportionally (pro rata between contributions & gains), and even if you did a Roth IRA conversion you'd still have a very small tax bill because only the gains are taxed. I think that it's a good compromise to enter December with $36K in the traditional TSP and just under $18K in the Roth TSP, because only the Roth TSP contribution limit seems to trigger the TSP's computers with a hard stop.
Some of us milbloggers sit around all day trying to reverse-engineer the TSP stories to figure out how the heck the TSP computers are programmed, because it sure isn't on their website or any other documents. One of these people is a CFP and the spouse of a very senior officer in a combat zone, and even that LES looks screwed up.
Another issue is that there seem to be very few people (under a dozen) who have the financial commitment to contribute more than the $18K limit during the deployment. Even when the Army was sending soldiers into the desert for year-long deployments, we bloggers never heard of anyone trying to reach the IRS 415(c) additional limit with tax-free pay. Now that DoD and the IRS have widened the definition of a combat zone (including direct support areas) and now that some servicemembers are actually stationed in them (Qatar) we're seeing more of this situation.
One milblogger is transferring to a combat support zone with plans to contribute 3 x $54K over the three calendar years that they're in an area. This will probably include opting in to the DoD Blended Retirement System in 2018, where DoD's matching contributions to their traditional TSP will become part of the annual $54K limit. We should have this process figured out by the end of 2018.
One of our ideas for that milblogger's transfer was to contribute just under $18K to the Roth TSP before they arrived, and then switch everything to the traditional TSP. It looks like your large contribution to the Roth TSP (for the right reasons) might have triggered the stop. Again, not that the TSP explains it via e-mail or even letter.
Thanks for keeping us posted on how it goes. Eventually enough people will be asking these questions for the TSP to start answering them.