You should be able to save a map in text format without errors. I do so in order to edit maps with excel macros, but before I use them on a D2 server I load them up in Artifex again (after removing some extra quotation marks that excel adds with wordpad) and save them as binary for use on the server.
Perhaps there is an issue with your Definitions file. Make sure you are using an OP definitions file. Search your hard disk for all instances of Definitions.txt that correspond to artifex and delete them. Then unzip artifex and the definitions.txt file from the build 36 OP serverkit to a new folder you will henceforth use as your map editor folder and start Artifex. (it should prompt you for the location of the definitions.txt file.)
It is possible that you are using a definitions.txt file referenced in the registry that persists from EAW map editing. Did you create your SS3 map from an old EAW map? If so you'll need to start fresh, or look at the differences in an EAW and OP map from the corresponding definitions files and make the appropriate edits to the text version of your map. (can be quite tricky - its best to start fresh).
You should only have one definitions.txt file present on your harddisk that Artifex references. I always just put Artifex in something like C:\MapEditor\ Then if I want to edit EAW maps or experiment with new terrain or empire definitions I rename the definitions.txt files so that the active one is always just "Definitions.txt".
e.g. here is a directory listing of my map editor folder:
Directory of C:\Map Editor
11/23/2005 03:43 PM <DIR> .
11/23/2005 03:43 PM <DIR> ..
02/07/2005 06:14 PM 32,568 43x22.mvm
02/07/2005 06:14 PM 1,162 43x22.zip
02/07/2005 08:35 PM 34,680 44x23.mvm
04/02/2001 05:36 PM 151,552 Artifex.exe
11/22/2005 07:00 PM 2,052 Definitions.txt
08/27/2005 10:23 PM <DIR> Definitions_new
08/17/2005 04:23 PM 2,255 Definitions_new.txt
08/27/2005 10:19 PM 932 Definitions_new.zip
04/19/2001 05:08 PM 1,967 Definitions_orig.txt
09/30/2004 08:41 PM 1,977 Definitions_rod.txt
11/22/2005 07:00 PM 2,052 Definitions_stockmap.txt
05/01/2001 11:21 AM 15,820 EarlyMap.mvm
11/22/2005 05:35 PM 55,807 EarlyMapt.mvm
06/01/2001 12:22 AM 40,024 FE.mvm
10/11/2004 11:57 AM 154,071 FEtext.mvm
02/24/2004 12:38 PM 39,376 fne01.mvm
02/24/2004 12:59 PM 39,376 fne02.mvm
02/26/2005 08:13 PM 57,784 HoMaster.mvm
09/14/2004 07:33 AM 196,087 KCW.mvm
09/26/2004 03:04 PM 196,087 KCW2.mvm
09/26/2004 03:04 PM 50,296 KCW2a.mvm
10/13/2004 06:41 PM 50,296 KCW2b.mvm
08/22/2005 04:59 PM 79,384 Map10.mvm
08/22/2005 04:59 PM 8,332 Map10.zip
08/24/2005 04:14 PM 79,384 Map11.mvm
08/24/2005 12:26 PM 314,308 Map11t.mvm
08/25/2005 05:26 PM 79,384 Map12.mvm
08/25/2005 05:26 PM 7,059 Map12.zip
08/25/2005 08:02 AM 314,308 Map12t.mvm
08/25/2005 08:02 AM 314,308 Map13t.mvm
11/22/2005 08:03 PM 313,878 Map14t.mvm
11/22/2005 11:23 PM 79,180 Map15.mvm
11/23/2005 01:03 PM 79,180 Map16.mvm
11/23/2005 03:04 PM 79,180 Map17.mvm
11/23/2005 03:32 PM 79,180 Map18.mvm
11/23/2005 03:43 PM 79,180 Map19.mvm
12/26/2003 01:04 PM 3,164 Map1t.mvm
03/15/2005 10:05 PM 79,096 Map3.mvm
08/17/2005 05:44 PM 314,078 Map3t.mvm
08/17/2005 05:43 PM 79,384 Map4.mvm
08/17/2005 06:09 PM 310,947 Map4t.mvm
08/17/2005 07:34 PM 314,710 map5t.mvm
08/17/2005 07:56 PM 79,384 Map6.mvm
08/17/2005 07:56 PM 8,389 Map6.zip
08/17/2005 07:43 PM 314,710 Map6t.mvm
08/22/2005 01:22 PM 79,384 Map7.mvm
08/22/2005 01:22 PM 314,702 Map7t.mvm
08/22/2005 03:55 PM 314,411 Map8t.mvm
08/22/2005 04:00 PM 79,384 Map9.mvm
08/22/2005 04:00 PM 8,326 Map9.zip
08/26/2005 01:39 PM 5,784 Map_n2.mvm
08/26/2005 02:29 PM 5,784 Map_n3.mvm
07/02/2001 09:46 AM 29,104 MediumMap.mvm
05/01/2001 11:27 AM 15,820 MiddleMap.mvm
11/22/2005 06:58 PM 31,232 new_terrain_to_old.xls
06/22/2004 05:38 PM 2,173 race01.mvm
06/22/2004 05:39 PM 2,173 race02.mvm
06/22/2004 05:41 PM 7,877 race03.mvm
06/22/2004 05:50 PM 21,093 race04.mvm
06/22/2004 05:54 PM 21,347 race05.mvm
06/22/2004 07:40 PM 7,096 race06.mvm
06/30/2004 04:41 PM 21,349 race06t.mvm
05/30/2001 09:24 AM 245 readme.txt
09/30/2004 08:53 PM 22,016 rodstest_bin.mvm
09/30/2004 08:53 PM 80,496 rodstest_text.mvm
02/22/2004 02:39 PM 22,008 sfbop01.mvm
02/22/2004 02:51 PM 22,008 sfbop02.mvm
02/22/2004 02:59 PM 22,008 sfbop03.mvm
02/22/2004 03:21 PM 22,008 sfbop04.mvm
02/22/2004 04:09 PM 22,008 sfbop05.mvm
02/22/2004 04:18 PM 22,008 sfbop06.mvm
02/22/2004 05:27 PM 22,008 sfbop07.mvm
02/22/2004 06:50 PM 22,008 sfbop08.mvm
10/22/2004 06:05 PM 39,376 sfbop09.mvm
02/20/2005 02:19 PM 150,133 sfbop09_text_test.mvm
02/15/2004 08:58 PM 55,807 SFBOPmap.mvm
10/01/2005 02:58 AM 53,496 SG5_Final.mvm
10/05/2005 07:57 AM 53,496 SG5_Final_2.mvm
10/05/2005 09:16 AM 53,496 SG5_Flatfile_Final.mvm
09/14/2005 06:52 PM 48,792 SG5_Test Map.mvm
09/30/2005 12:48 PM 53,496 SG5_testmap_2.mvm
09/30/2005 07:08 PM 53,496 SG5_testmap_2a.mvm
08/23/2005 08:35 AM 502 Shortcut to Artifex.exe.lnk
01/22/2004 10:33 AM 5,580 Small10x10.mvm
11/19/2003 11:30 PM 23,768 TourneyMap2.mvm
12/26/2003 01:00 PM 89,964 TourneyMap2t.mvm
12/26/2003 02:04 PM 27,384 TourneyMap3b.mvm
12/26/2003 02:04 PM 102,987 TourneyMap3t.mvm
12/31/2003 05:52 PM 27,384 TourneyMap4b.mvm
12/31/2003 05:52 PM 102,486 TourneyMap4t.mvm
89 File(s) 6,723,831 bytes
3 Dir(s) 24,402,919,424 bytes free
Clear as mud?
Also, if I might reccomend saving more frequently than every three hours, and save mutliple versions as you go so you can go back if desired.