Matlab is stalling after every command

I am processing relatively large data sets ~1000x200000 int16 with Matlab 2012b (64bit). I have more than enough RAM; there are 20Gb free. Every time I type a command, no matter how simple, matlab drives up the CPU usage to >100% (multicore) and stalls for about 10 seconds. This is extremely frustrating and time consuming. I have tried multiple restarts but to no avail. Any help is much appreciated.

[Walter Roberson]

Do you have the Variable Editor window displayed? If so try turning it off.

[Alec]

Could it be that your current directory has many (>30000) files? I ran into this issue when generating lots of data files. Clearing/moving these files out of the working path fixed my issue.