This is almost certainly the problem, disk IO speed.  Also the fact that your system is reporting low ram allocation that doesn't mean it's not doing paging.  The OS may not be using all the available ram, and it may be reserving parts of it.

You can try using iostat and iotop to monitory what's going on.  Also check your memory usage settings. and if possible adjust your cache size.

My money is on your disk is just too slow.

And remember that when something is bottlenecked it can run perfectly fine until the straw that broke the camel's back comes along and you go from running fine to massively bottlednecked and paging like crazy.