Bitcoin block backlog problems

As I mentioned in a recent blog post for security reasons I do not recommend running Bitcoin clients online 24×7. However the net effect of this is a block backlog and longer time to clear new transactions. This happened to me earlier in the week when I managed to get 1000 blocks behind (not much really since 10 blocks per hour normally get created).

When processing the backlog my client seemed to get stuck on one block for a long time and I was wondering whether this was related to the number of transactions over the last week (Mt.Gox saga!) and as a result a greater proof of work?

If this is the case e.g. blocks with a large number of transactions incur a larger proof of work and hence backlog processing time, there may be trouble ahead! Imagine banks changing their clearing times due to transaction volume.