If you did not have any issues previously, you should not worry about it as you have discovered that the behavior has not changed. The recent change is only about making the ordering take effect sooner (before MC restart).
Imagine this, you have channel 1 which you prefer using tuner A. Now by setting tuner A on top of the priority list, all you have achieved is to guarantee that tuner A will be loaded when you play any other channels (Channel 2, 3, 4 etc.) Once tuner A is loaded for channel 2, it is not available for channel 1. That defeats the purpose of setting tuner A as channel 1's preferred tuner.
By automatically moving tuners that are preferred by some channels to the bottom of the list, you reserve the tuners for those channels that prefer them. You simply can not set a tuner at the top of the list for all channels while still try to reserve it for a few particular channels.
Also you definitely do not need to worry about your STB (Colossus) at all. Priority of tuners only apply to tuners of the same type. And it makes sense only if you have multiple tuners that can serve the same channel. For your STB channels, each of them must use your Colossus, regardless where you put the Colossus on the list. Your other (non-STB) channels types will never touch the Colossus.