It sounds like the file path for your swatch tables is wrong. Flexi is looking for a swatch table on a folder that either doesn't exist or doesn't contain the swatch table(s).
I don't have Flexi on this machine. So, I'm going from memory here. But you should be able to go to View>Open Swatch Table and direct Flexi to the folder with your swatch table. The default should be something like Programs>Flexi>Swatch>Tables. You can direct it to any folder where you have your swatch tables saved. Once you open the table, you should be able to close Flexi. When you reopen, it will remember the last table you opened and its location.
Hope this helps.