If you are transferring 100 why are you only setting 50 as teh lot?
Set teh quantity to ship to be 50 if this is the case.
Don't go into tables and delete entries - have you not learnt this causes you issues?
There have been issues in this area, but it sounds more like yours are knowledge - you also do not post what the error is, I would guess it told you you had defined tracking lines for 50 of the 100, so it wants anoher 50 to ship, unless you set teh quantity to ship.