I had a similar experience last night: installed SH3 Commander and IUB 1.02 and all went well initially. Then discovered a newer version of SH3 Commander and, after having manually installing a few other mods, decided to go with a clean reinstall of everything but no IUB showed up. I was playing around with a lot of things last night so I'm not 100% sure that this was what brought it back but I did a SH3 Commander rollback, removed IUB using JSGME, and then readded IUB with JSGME and all was well.
This morning I discovered IUB 1.03 and repeated a similar procedure to upgrade to it (SH3 Commander rollback, IUB 1.02 removal via JSGME followed by JSGME addition of IUB 1.03) and no problems.
In fact my only (minor) gripe is the "realistic" crew it forces (via its RUB component), not unique to 1.03 though, as I'm used to the generic SH3 crew and prefer it (and no changes I make in SH3 Commander seem to eliminate it). Oh well, the vastly improved everything greatly make up for this one little gripe of mine.
Good luck to you, I'm sure whatever's causing its nonappearance is something minor and well worth rooting out.
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