Did you activated "Just-in-Time Synchronization (JITS)" on netfolders? And with what values? Did you enable indexing?

Have you enabled monitoring for the Filr server (CPU use)? You can run a report (file use) and look if the files are from a specific directory (specific time during high processor load).

I myself had problems with high cpu load during the automatic (every night) indexing process. This was resolved after an update from Filr.

I have also heard someone who makes less resources available for a process (max 50% from cpu) but of course these are workarrounds.