I guess I've hit one of those bug in the April 24th version as well. Just in case this isn't one of them, I'm posting the log here.
I've built another base, then saved:
]version
"version" is "UFO: Alien Invasion 2.1.1 x86 Apr 24 2007 Win32 DEBUG"
CL_UpdateHireVar()... aircraft idx: 0, homebase: PHALANX HQ
CL_UpdateHireVar()... aircraft idx: 2, homebase: Base #2
Save 'slot6'
...subsystem 'base' - saved 11607 bytes
...subsystem 'campaign' - saved 288 bytes
...subsystem 'hospital' - saved 2 bytes
...subsystem 'market' - saved 2176 bytes
...subsystem 'research' - saved 6331 bytes
...subsystem 'employee' - saved 28459 bytes
...subsystem 'aliencont' - saved 0 bytes
...subsystem 'production' - saved 22 bytes
...subsystem 'aircraft' - saved 1 bytes
...subsystem 'messagesystem' - saved 26811 bytes
...subsystem 'stats' - saved 28 bytes
...subsystem 'nations' - saved 32 bytes
Campaign 'Shai31' saved.
Then I tried to load it. I hit the "Error in loading a subsystem" error again.
Loading savegame
...version: 1
...game version: 2.1.1
Global data loaded - size (null)u bytes
...techs: 132
...buildings: 18
...ranks: 8
...nations: 8
Load 'slot6'
...subsystem 'base' - loaded 11607 bytes
Initializing aircraft and aircraft-items ...
...aircraft and aircraft-items inited
Cmd_AddCommand: popup_aircraft_action_click already defined
Cmd_AddCommand: ships_click already defined
Cmd_AddCommand: ships_rclick already defined
Cmd_AddCommand: multi_select_click already defined
Activate stage intro
...subsystem 'campaign' - loaded 288 bytes
...subsystem 'hospital' - loaded 2 bytes
...subsystem 'market' - loaded 2176 bytes
...subsystem 'research' - loaded 6331 bytes
...subsystem 'employee' - loaded 28459 bytes
...subsystem 'aliencont' - loaded 0 bytes
...subsystem 'production' - loaded 22 bytes
...subsystem 'aircraft' - loaded 1 bytes
...subsystem 'messagesystem' - loaded 26844 bytes
...subsystem 'messagesystem' could not be loaded correctly - savegame might be broken (3f)
Changing to Singleplayer
I hope the new version already have a fix for this.
Edit:
I hit the "Assertion failed!" bug with the April 24th version. It seems it is somehow related to having more than 1 base, and maybe more than 1 radar station, but I can't be sure. I'll try to reproduce the bug.
Here is the log:
Loading a working saved game:
Load 'slot5'
...subsystem 'base' - loaded 11479 bytes
Initializing aircraft and aircraft-items ...
...aircraft and aircraft-items inited
Cmd_AddCommand: popup_aircraft_action_click already defined
Cmd_AddCommand: ships_click already defined
Cmd_AddCommand: ships_rclick already defined
Cmd_AddCommand: multi_select_click already defined
Activate stage intro
...subsystem 'campaign' - loaded 244 bytes
...subsystem 'hospital' - loaded 6 bytes
...subsystem 'market' - loaded 2176 bytes
...subsystem 'research' - loaded 6331 bytes
...subsystem 'employee' - loaded 24022 bytes
...subsystem 'aliencont' - loaded 0 bytes
...subsystem 'production' - loaded 22 bytes
...subsystem 'aircraft' - loaded 1 bytes
...subsystem 'messagesystem' - loaded 23353 bytes
...subsystem 'stats' - loaded 28 bytes
...subsystem 'nations' - loaded 32 bytes
File 'slot5' loaded.
Changing to Singleplayer
Built another radar station in the second base, let the time run. I saved when a mission popped-up:
CL_UpdateHireVar()... aircraft idx: 0, homebase: PHALANX HQ
CL_UpdateHireVar()... aircraft idx: 0, homebase: PHALANX HQ
CL_UpdateHireVar()... aircraft idx: 0, homebase: PHALANX HQ
CL_UpdateHireVar()... aircraft idx: 2, homebase: Base #2
CL_UpdateHireVar()... aircraft idx: 0, homebase: PHALANX HQ
Save 'slot7'
...subsystem 'base' - saved 11607 bytes
...subsystem 'campaign' - saved 292 bytes
...subsystem 'hospital' - saved 2 bytes
...subsystem 'market' - saved 2176 bytes
...subsystem 'research' - saved 6331 bytes
...subsystem 'employee' - saved 28450 bytes
...subsystem 'aliencont' - saved 0 bytes
...subsystem 'production' - saved 22 bytes
...subsystem 'aircraft' - saved 1 bytes
...subsystem 'messagesystem' - saved 26811 bytes
...subsystem 'stats' - saved 28 bytes
...subsystem 'nations' - saved 32 bytes
Campaign 'Shai31-2' saved.
I then tried to reload the game I just saved:
Loading savegame
...version: 1
...game version: 2.1.1
Global data loaded - size (null)u bytes
...techs: 132
...buildings: 18
...ranks: 8
...nations: 8
Load 'slot7'
...subsystem 'base' - loaded 11607 bytes
Initializing aircraft and aircraft-items ...
...aircraft and aircraft-items inited
Cmd_AddCommand: popup_aircraft_action_click already defined
Cmd_AddCommand: ships_click already defined
Cmd_AddCommand: ships_rclick already defined
Cmd_AddCommand: multi_select_click already defined
Activate stage intro
...subsystem 'campaign' - loaded 292 bytes
...subsystem 'hospital' - loaded 2 bytes
...subsystem 'market' - loaded 2176 bytes
...subsystem 'research' - loaded 6331 bytes
...subsystem 'employee' - loaded 28450 bytes
...subsystem 'aliencont' - loaded 0 bytes
...subsystem 'production' - loaded 22 bytes
...subsystem 'aircraft' - loaded 1 bytes
But then I hit that "Assertion failed!" bug.