"They said the reason that my Traditional IRA value is now $6,500 and (not $6,000) is because the calculations on gains/losses are based on my entire ROTH IRA portfolio."
Yes, that is what is required by the tax code. Your contribution is to the IRA, not to any particular investment in the IRA (even though you use the contributed cash to purchase particular investments within the IRA). You have a $500 taxable gain attributable to your $6,000 contribution, not a loss:
https://www.law.cornell.edu/cfr/text/26/1.408-11
