So, I popped into the IRC channel with this issue. I have a reactor setup, and while I was in the process of getting it fully fueled, I converted some cyanite int bluetonium. The reactor's initial fuel I had put in was yellorium, and I know in 1.6.4 that you are able to put both into the reactor at the same time as they were both treated the same in regards to fuel goes. Well, when I attempted to put the bluetonium into the reactor to help top it off, the reactor refused to pull the fuel in. I was informed in the irc channel by another "guest" that "[22:03] you can't mix fuels Gunner76th".

My question/comment is this: 1) is this true that you cannot put bluetonium into a reactor that currently has yellorium fuel in it or vice versa 2) if this is the actual case, why? This means that if you are someone that only has a need for a single reactor, the cyanite waste product and by extension, the bluetonium fuel that could be created from it is a useless item within the game. If in fact you can only use bluetonium in the reactor once all of the yellorium has burned up, this means that, 1) you cannot setup a method to recycle the cyanite into bluetonium and feed it back into the reactor 2) if you do decide to use bluetonium fuel, your reactor must first be completely out of fuel, at which time it could cease to produce steam/power and cause your entire system to fail.

Yes, I understand that you could in theory use multiple reactor access ports, 1 for yellorium input and 1 for bluetonium input, so that once the reactor runs out of yellorium it would refuel with the bluetonium, but that still does not address the fact that, as fuel level inside the reactor decreases, so does its energy/steam production ability, and by extension, have the potential of causing a power systems crash for your entire setup.

You can't mix stacks of yellorium and blutonium ingots, just like you can't mix stacks of any other two distinct items. However, as a fuel (i.e. inside a reactor's actual fuel tanks), they should mix just fine. Blutonium currently is aliased to yellorium's fuel data, so it's treated identically by the fuel tanks - in fact, it transforms into yellorium when it enters the fuel tank.

I may have broken that in 0.4. If so, that's a bug.

So, direct answers to your questions:
(1) No. You can put blutonium into a reactor which has yellorium in it. If it doesn't work, that's a bug.
(2) See 1.

I'll investigate your report of being unable to put blutonium into a reactor which already has some yellorium in it, tonight.

Reproduced. This is a bug.

Fixed by 59b3897 (I tagged the wrong issue in the commit. Derp.)