Is your Mods folder in the TS3 user game folder in Docments? Back in 2009, mods were installed a different way within the Program Files, but that changed with Patch 1.12 somewhere the next year.
There's a couple of mods that, by design, suppress that dialog box so it no longer shows on startup. One is an NRaas mod that we are not allowed to mention here, the other is AwesomeMod. Might either one be in play? But the pop-up dialog is only one indicator that the mods are loading, failing to appear doesn't mean anything is wrong. Also that scrips dialog was never capable of listing all script mods for those who have lots of them, it always cut itself off after a while and the mods that never got listed load anyway.
Do these script mods you are using have no command menus or noticeable presence in the game that you can check on? Most NRaas mods, for instance, have options menus so that an NRaas menu appears on City Hall, if not on sims, objects, and lots.
