Created attachment 340209 [details]
screendump1

This happens in 2.6.14 in Windows 10 and 2.6.9 in Debian 8.5.

If after scrubbing a security account you decide it is not what you want (say you have incorrectly linked splits to a lot), then you delete the capital gains transactions created by scrubbing (without first cleaning up the lots), then go into the Lots in Account window and click on a lot, it seems to try to recreate the cap gain transactions again but they are incorrect. 

For example:
1) create following transactions:
 1/1/2015 Buy  100 @ $10.00 ea = $1000.00		Lot 0
 1/2/2015 Sell  10 @ $11.00 ea = $110.00-
 1/3/2015 Buy  100 @ $12.00 ea = $1200.00		Lot 1
 1/4/2015 Sell 150 @ $13.00 ea = $1950.00-
See attached screendump: 1BeforeInitialScrubAccount.png

2)
Scrub Account correctly creates 3 cap gains transactions:
 1/2/2015 Lot 0 gain = sell 10 x 11.00 - buy 10 x 10.00 =  110.00 - 100.00 =  10.00
 1/4/2015 Lot 0 gain = sell 90 x 13.00 - buy 90 x 10.00 = 1170.00 - 900.00 = 270.00
 1/4/2015 Lot 1 gain = sell 60 x 13.00 - buy 60 x 12.00 =  780.00 - 720.00 =  60.00
See attached screendump: 2AfterInitalScrubAcct.png

3)
Delete the 3 capital gains transactions.
See attached screendump: 3AfterDeletingCapGainTrans.png

4)
Go into the Lots in Account window and click on lot 0. This creates:
 2 capital gain transactions for 1/2/2015 each with value $10.00
 1 capital gain transaction for  1/4/2015 with value $260.00
See attached screendump: 4AfterClickOnLot0.png

5) If you reset the lots and transactions to how they were just before point 4,
then click on lot 1, this creates:
 2 capital gain transactions for 1/4/2015 each with value $60.00
See attached screendump: 5AfterClickOnLot1.png

The correct procedure would seem be to delete the lots first (or at least unlink the sell splits from the lots), before deleting the capital gain transactions. I have found no problem when doing this.

I suspect this will be difficult to fix and there will not be much motivation for it to be fixed given the easy work-around, but I wanted to document it anyway.
I intend to update my recent documentation to specify that lots should be deleted or at least sell splits unlinked from the lots before deleting the capital gains transactions.