OK. When the laptop boots up , it uses dos mode graphics. Its low bandwith and very little data is flowing down the cable. When windows starts up all the funky graphics start and the refresh rate may change. The amount of data going down the cable just went thru the roof.
Before you modified the cable it was quite well matched to what was needed from it , some of the wires may have been twisted together to cut down on noise from other wires. Now you come along and splice in a lump of idc cable with all the wires in a row and 'crosstalking' like mad.
What you may want to try is spliting the idc into single wires and making them a bit more 'random' , it would reduce the effect of any one wire on any other wire. If any of the wires were twisted together , try to continue the twist thru your extension cable.
Last time I tried this I had to sheild half the wires and ended up with a cable the thickness of your thumb (and about as flexable) , but it did work.