Default Rom Customisation & Modification (PLEASE HELP!)

Hi Guys

I need some basic help/understanding about Android ROM modification.

In particular for an Android MX TV Box - but the questions is generic and applies to any ROM I guess.

The Rom im flashing has the following files (and works perfectly):

factory_update_param.aml
hd18d_mx4.zip
recovery.img

I am able to successfully restore my box with this image (so I know that the image is working fine).

Within the hd18d_mx4.zip there is:

Directotories: data, META-INF, recovery, system
files: boot.img, bootloaded.img, logo.img

I tried to do a very basic step of deleting a single system.apk file from the system/app folder (no other changes) and I am unable to flash this firmware.

Any ides - what am i doing wrong?? It seems like i cant make any modifications to the zip file or there are problems.

I tried using dsixda Rom kitchen, and even if put rom in working directory, and then immediately

Please help - this is driving me mad!! Aaarrghghg