Integration Services :: SSIS Data Transfer Says Rows Copied But Count On Table Is Less?

I've a SSIS 2008  parent/child package solution to manage data transfers between two different data sources, so we can copy multiple tables and capture how many rows were transferred and duration for each transfer.  This solution was working fine up until last week, when I made some changes to allow the package to perform a source count using standard SQL determined by an expression, or SQL provided from configuration tables, I also changed the package to Truncate or not the destination table, again controlled by configuration settings in a table. The child packages which perform the data flows have not changed!

The day after the controlling package promotion to live, I saw the bizarre behaviour of the Package log stating all rows transferred, but the actual table counts were not what the log stated, see attached file. The package solution works ok on other servers and was ok in DEV, but there were less tables and rows transferred.Re-running the package gave the same errors, but on some of the same tables and some different ones. 

As it is the child packages doing the transfers and nothing has changed in them. I cannot see how the log would be able to say all rows are transferred and yet not all of the rows are actually moved?

Process output - where you can see counts and log Table transfer controller (as txt not dtsx)

An example of the data transfer child packages (as txt not dtsx)When I set the ExecuteOutOfProcess = True the package worked fine, unfortunately, this is not a good solution as SSIS 2008 does not tidy up the Dtshost.exe processes it starts and I'd be left with a memory issue after a very short time, we transfer hundreds of tables each day. ( I could write a .net script in the controlling package to kill the child processes, but that would still have hundreds of processes running before I could end them, as we have three parallel streams to allow a bit better performance.