Speed doesn't really come into it. Most avionics still use X86 chips because the computing requirements are well below that needed by the average PC. A lot of these older chips are no longer available for which one solution is to rehost the software on to Pentiums or similar. The problem with this is that the code may not work without a LOT of modifications. Brand H ran into this big time when they did their Gen Av programme a few years back and it took a long time to get all the bugs out even with - or maybe because of - autocoding. Don't forget that for any critical task you have to requalify the software to DO-178B which can be horrendously expensive.
One of the additional problems with FMCs is that, because of the CDU interface, they're getting a lot of tasks for which they were not designed. This means that not only must the new software be qualified to an appropriate level (more critical = more testing)but also the original core might need to be updated too if its level is no longer appropriate.