There’s definitely a conflict; Magic Item Compendium has things reversed compared to Dungeon Master’s Guide. The errata specifies that the “primary source” should win the cases of such a conflict.
Now the question is, which source is primary? That’s not an easy question. Usually the place where a thing is originally defined in full is the primary source, but Magic Item Compendium (along with Spell Compendium and Rules Compendium) assert their own primacy. They explicitly attempt to “take over” for previous books, not just compiling and organizing, but also updating and refining the material they hold.
There is a considerable debate about this assertion. From a strict-RAW perspective, it is problematic. However, I will say that in my experience, most do treat the Compendiums as primary.
The other issue, from a non-RAW perspective, is the probability that this swap was a mistake. It’s not called out as an intentional change, and it would be very easy to transpose the two ideas.
Ultimately, then, I recommend going with Dungeon Master’s Guide on this – not because it’s primary, but because its version is the better rule. Doubling the cost of the mundane weapon is minor; doubling the cost of the scaling magical enhancements is huge. The cost of iron weapons is extreme, far more than it ought to be, and the Dungeon Master’s Guide rule leads to lower prices. Probably still too high, but lower here is better.