Start by pressing the Clear All button from the Cache tab in Preferences.
Close Preferences. Select the A_thaliana_Jun_2009 genome and click Load Sequence.
Select Yes to cache the sequence.
Adjust the Max Cache Size to 15 MB, then click Apply.
Now remove the 2bit file (29 MB) from the cache by highlighting the file and clicking Remove.
Adjust the Max Cache Size to 15 MB, then click Apply.
Select the A_thaliana_Jun_2009 genome and press the Load Sequence button (again) and select Yes (again).
Select Reset Cache Preferences and hit Refresh to update the Max Cache Size value.