It would be useful to know which Incognito firmware is being used and whether or not internal (PBI) high-speed SIO is enabled for those titles which fail to load via SIO2xxx devices. Regarding the problem titles, most or all exhibit identical behaviour on U1MB systems (which is hardly surprising given that Incognito's XL/XE mode emulates exactly the same operating environment).
1. Boogie Nights (XEX) may be incompatible with the SIO2SD boot loader. I don't have SIO2SD to hand right now, so can't confirm.
2. Overmind (ATR) hangs on an U1MB when run from the CF card too. Possibly it relies on some property of being loaded from a serial peripheral.
3. Bitter reality (ATR) encounters a disk error on an U1MB machine when run from the CF card, probably also because it provides its own built-in serial loader.
4. Phantasy (ATR) crashes when loaded from the CF card on an U1MB machine (reasons unknown).
Any ATR which chooses to load itself via a custom SIO loader will always fail when launched from the CF card. The ATR handler is only compatible with software which employs standard calls to DSKINV/SIOV.