Hey Sparky64,
I know what I am about to say is probably pretty obvious, but I think it warrents being said anyway.
Get ahold of all the written specs that were given by your company to the supplier. Make sure you have read them and understand exactly what was agreed upon.
Then get ahold of the proposal and any/all approval drawings and documentation. Check them against the specs. Obviously any discrepancies between the two will need to be investigated and ironed out in your organization first (and should have been prior to the order being placed, but may not have been).
Now that you know what you are SUPPOSE to be getting, check it out thoroughly. Make your supplier prove it to you. Measure foot prints, check wire numbers, clock cycle times, verify wire sizes, observe that each and every button does exactly what they say it does, disable sensors and observe the response, verify that every component is precisely the ones that were specified. In short, try to look at everything. One good way is have all your maintenance guys go over it with a fine tooth comb. You will get a lot of opinions you might rather not hear, but on the other hand, you might spot a bad weld or poor wiring practices, too.
And if you are allowed (by your organization especially) make the supplier run the machine for a specified period without ANY hiccups. To do this you will need to supply constant observation. If provisions for this were not in the original agreement, you may be out of luck, but I would try it anyway.
The more you can do like this the better. Not only will you uncover a lot of little problems, you will create a bargaining chip your company might be able to use to reduce some up-front costs or to get some additional features thrown in for nothing.
I have been on both sides of this this particular coin and this type of commissionings is very valuable.
My .02 worth.
Steve