The builder is still changing damage expressions on custom creatures. I can not nail down specifically what triggers the change. It does not appear to be the problem with fractional average damage that was previously the problem.
Average damage stays the same and the dice expression changes. It effects some custom creatures and not others and happens only sometimes to the ones it effects. It seems only to happen when re-launching the builder. I typically customize official creatures as opposed to creating them from scratch and this may play a part in the issue.
The custom creature below has changed the last three times I have edited it to correct the problem and looked at it a day later. The damage expression for Silver Longsword was entered at 2d8 + 11 and Heavy Crossbow at 2d10 + 7. This is the most recent change to the expression made by the builder, but it has changed it twice recently. I list it case anyone with authority would like to look at the file on my account to help resolve the issue.
I've noticed this behavior too, and not just with custom monsters. I was preparing to run an adventure from Dungeon Mag. when I noticed it happening to "Morgana, Priest of Torog" originally published in Dungeon Mag 171. The compendium/original publication and monster builder damage expressions do not match.
That is interesting, in an unhappy way. The average damage field and the damage expression field are linked. That seems to force a calculation for some reason at some times that changes the damage expression field.
It should only calculate a new damage expression when the user changes the average damage and at no other time. It is unnerving to have an application changing your entries. 