Version:           3.97.2 svn 1121075 (using KDE 4.3.5)
Installed from:    openSUSE RPMs

I think there may be two or three separate issues here.
I wanted to reconcile a banking account, which previously had been reconciled a month ago.  Only three items had been added in the meantime.

However, both the starting and finishing balances were £32000 too high.  Looking back, I found that a number of items that must have been reconciled correctly last month, no longer were marked reconciled.  As the account had previously been reconciled correctly, and as the now unreconciled items were spread out, I decided to do a 'block' reconcile of the whole account apart from the three new entries, which are marked clear.  When I then went to reconcile again, nothing had changed, and I realised that the block reconcile had done nothing.  This is because of the previously reported problem of context menu selection clearing selected status.

I found the keyboard shortcut to mark as reconciled - ctrl+shift+space - but that also did nothing, and I realised that that shortcut, which is available in v1.03, is not in 3.97.

So, I have to revert to v1.03 to reconcile.

Now, I look to see why the entries had become unreconciled.  They now appear to have a monetary value as their payee,which is obviously wrong, but on opening them this turns out to be from a memo, and the payee is blank.

What else they have in common, is that the payee they should have had is the one I was attempting to change when KMM crashed last night.