It's Not About The Size
Although problems with compatibility between motherboards and processors are often associated with 45nm parts, it is worth noting that it is not the 45nm process itself which causes problems. Incompatibility occurs because the BIOS of a motherboard is not able to predict the future. While motherboard manufacturers will attempt to anticipate what kind of processors will debut, their ability to do so is limited. When a new iteration of an established architecture comes along, it is quite possible that previous motherboards won't recognize the processor because the BIOS has no way of knowing what the processor is.
You can fix this yourself by upgrading the BIOS (see next page), provided the motherboard manufacturer makes one available. Sometime, the CPU architecture changes by enough that despite having the right socket, an older motherboard just won't be able to run the new processor. A quirk of most Nvidia 680i based boards, for instance, is that you can upgrade the BIOS to make them run a Core 2 Duo, but not a Core 2 Quad.
The problem, then, is not in the processor. If you're afraid of buying a 45nm processor because you've heard of issues with them, don't fear. The incompatibly is not random, but rather is caused by a known issue. As such, it can easily be anticipated and avoided. That said, there is the possibility that your current motherboard will not be at all compatible with a new processor, in which cause an upgrade will be impossible. Through proper research, you can discover whether or not an upgrade is possible with one hundred percent certainty.