I have a long-term investment account that has a stock (JDSU) in it that has significant losses. I am going to sell that stock to generate a tax loss for this year to balance out my gains. I have another account, ShareBuilder, that automatically invests once a month, JDSU is one of the stocks that is part of my ShareBuilder Plan. Is the wash rule going to take a chunk out of my long-term sale for loss?

Yep. Having the stocks in two different brokerage accounts doesn't shelter you from the wash sale rules.

You could stop the purchase for 30 days after the sale to limit the issue. It is too late to do anything about the purchase that happened recently (late Nov/early Dec).

Assuming that you are purchasing smaller quantities each month, just sell what you need to get your desired loss PLUS the number of shares you just purchased in the 30 days before the sale. The wash rules will disallow the loss on the shares you recently purchased, but the rest will be allowed. If you didn't want to stop the upcoming purchase, you could add that number of shares to the sale.

--Peter