Always best to use full-frame uncompressed for the initial output if you intend to perform video editing in post production, as you will always lose additional quality when recompressing after post production.

The root of the problem is the inability of your current video editing software to handle the output. On recent Windows graphics implementations the uncompressed output is probably 32 bits (4 bytes) per pixel. A bit of arithmetic comparing the frame dimensions and the number of frames with the byte size of output should tell you how many bytes are being used for each pixel.

A lot of older video editing software (eg. Corel) can only handle 24 bit true colour.

My advice is look around for alternative software (eg. JASC Animation Shop or AVIEdit) which can handle 32 bits, or any freeware that can convert from a 32 bit to a 24 bit format so that you can use your existing editing tools. These will also reduce the size of your uncompressed output files by 33% or so.