I acted on Harlans comment about using the vmoptions file to set the VM max memory to 256. Certainly seemed to speed things up. Didn't get back any of the missing files. I am in the process of moving to a new Brain.
While monitoring the memory use I noticed that it runs at around 124Mb now but that the actual memory in use cycles from 124 to 116 as teh garbage collector runs. This is normal for a JVM but it happens even if there I am not doing anything in the brain. Could be a background process but could also be a leak?
Also tried setting the minimum to 128 as well as the max to 256, seems to boot a bit faster. This technique can also be used to avoide memory paging in Windows based systems when both the min and max are set to a predetermined amount, it just means that the VM will grab all its memory at start up. This can be useful in systems with lower amounts of RAM.
My PersonalBrain.vmoptions now looks like:

It appears to be important that the values are on seperate lines and each line ends with a linefeed

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