I hope I am correct in assuming the following:
My 401K has both after-tax contributions and pre-tax. After I leave the company, I can elect to rollover my pre-tax to an IRA, and have a separate check sent to me for the after-tax contributions. The after-tax check is free and clear of any tax liabilities, and also does not need to be reported on any tax forms, such as 8606, and 1040. This is what my company has told me, but I want to be 100% sure. This would make more sense to me, than rolling over the after-tax money into an IRA.
Any thoughts would be greatly appreciated.

You will still be taxed for any accumulated earnings.

They are right.

The accumulated earnings on the post tax contributions should be included in the check representing the pre-tax amount.