OK, I searched the forum and found a link to Inez Diaz original help page for TOOL:
<a href="http://home.arcor.de/swigard/Downloads/TOOL/Help/" target="_blank">http://home.arcor.de/swigard/Downloads/TOOL/Help/</a>
In that one, under Ship Import, it says to also check the <i>Ship/Item/Location</i> checkbox when working with ships. This apparently sets the "u4" value to 0 (I think this is an indicator for weapons on characters - the default value of 4). Note that the "u4"value is ONLY used on a conversion from VRML files, so theoretically, it should have no effect on opening a GM file, editing it and exporting it back to a GM file.
I'm also wondering (out loud) if this combination of <i>Ship/Item/Location</i> checkbox and <i>Reverse Normals</i> checkbox has something to do with the reversed lighting issue seen on conversions from 3DS->VRML->GM.
<!--quoteo--><div class='quotetop'>QUOTE</div><div class='quotemain'><!--quotec-->Ship Import
For ship import check the Ship/Item/Location checkbox. That sets the u4 value to 0 and unchecks the Reverse Normals checkBox, as is usually required for ships. On unchecking ship, those values are reset to their defaults.
To work in the game with sails etc., ship models need a set of locators. The Easiest way to put those in is by loading a model from the game and saving its locators to a text file (via the locators menu). Then load your new model and import the locators form that text file (again via the locators menu). The view / locators menu allows you to edit the locators for the purposes of the new ship (see Locators).<!--QuoteEnd--></div><!--QuoteEEnd-->
Also, the beeping in game does appear to be from missing data (possibly collision data?).
<!--quoteo--><div class='quotetop'>QUOTE</div><div class='quotemain'><!--quotec-->NOTE:
Ships have some extra information in them that other models don't. For VRML models that information is generated by the tool, but not correctly - which results in the computer beeping once when loading such a model at sea. About further consequences I'm not sure. The tool will prompt you for an existing model to copy the missing data from. If you just cancel that dialog, the data will be generated.<!--QuoteEnd--></div><!--QuoteEEnd-->
I'm not sure if some of the problems mentioned here have been caused from opening converted VRML models or GM models, but this does appear to be a known problem with TOOL. It appears that a work-around for VRML models is to use collision data from an existing ship.
Lastly, I just tried using the Ship/Item/Location checkbox, and the filesize was the same as when the checkbox was unchecked.
kevin