OK, fixed in 1.1.5.
Scrapped the ore detection algorithm almost entirely. It still searches for minable resources, but saves and later uses the resultant ores for the sake of icons and such. It also saves ores with some additional information, such as required fluid (name and amount) as well as colour (pulled from the resource map colour). This allowed me to include ores of my own fairly easily, so this now also supports Holmium.
I wanted to include "ore enrichment", but it's going to take longer to put together and I didn't see the point in delaying the bugfix, so... 1.1.5 is the fix, 1.2.1 some time in the next few days with ore enrichment. And after that, who knows... maybe I'll add support for fluids, though there aren't that many minable ones in Base + Space Exploration.
edit Incidentally, this also natively fixed the conflict with Tiberium Wars, which had the same issue. Should also natively fix the conflict with Rainbow Ores, though I'm leaving the fix for that in as it only makes sense to check for both "icon" and "icons".
See, folks? This is what happens when you help us mod makers out a little :)