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Thanks TripleG, I was so excited because I thought I had cracked the code, but I guess not! :)

You are thinking about it wrong. Let me give an example of how it works:

You have a stallion who is Black White Spotted (White 8) Tobiano on DNA set 1 and Chestnut Roan Sabino (sabino 1) on DNA set 2. A simple version of what his DNA sets look like might look like this:

DNA set 1: Extension: E/E, KIT: W8/TO
DNA set 2: Extension: e/e, KIT: R/SB1

He can only pass 1 allele for each gene on to his foals. 1 Extension allele, either E or e, and 1 KIT allele either W8, TO, R or SB1. The 2nd allele the foal receives will come from his mother.

Scenario 1:
Say you have the inheritance chance for each of these DNA sets at 50%.
DNA set 1: Extension: E/E, KIT: W8/TO 50%
DNA set 2: Extension: e/e, KIT: R/SB1 50%
That means the foals are equally as likely to get the alleles from DNA set 1 as they are to get the alleles from DNA set 2. There is an equal chance he will pass along E or e for extension, and an equal chance he will pass along W8, TO, R or SB1 for KIT to his foals.

Scenario 2:
Say instead you have altered the inheritance chance for each of these DNA sets so that DNA set 1 is 100% and DNA set 2 is 0%.
DNA set 1: Extension: E/E, KIT: W8/TO 100%
DNA set 2: Extension: e/e, KIT: R/SB1 0%
You have basically forced the inheritance that 100% of the time the alleles that the stallion can pass along to his foals MUST come from DNA set one. That means the foals cannot inherit the e, R or SB1 from DNA set 2. They will always inherit the E from DNA set 1, and they are equally as likely to get either W8 or TO from DNA Set 1.

Just want to confirm that what RAM posted is 100% correct.