It sounds like you exported the .mdl to a folder somewhere and then imported it into SBuilderX. That's fine - the first time - but when you do that SBX copies the .mdl to the SBuilderX314\Mdls folder apparently to make it available for future placements. My guess is when you added the .mdl the 2nd time you again navigated to the folder that you originally exported it to and then SBX threw the error when it tried to copy the .mdl to SBuilderX314\Mdls again but found that there was already a .mdl there by that filename. You could just add the .mdl from the SBuilderX314\Mdls folder the 2nd and 3rd times (for me the browse dialog defaults to that folder anyway) and I don't think you'll see that error.
OK, I
think that takes care of the error you posted above but the next problem is I think you've found a bug in SBuilderX! When you finally do get your three objects placed in SBX and go to compile the .bgl I think you're going to see bglcomp throw an error also. This is because SBuilderX seems to be placing three instances of the <ModelData /> in the XML.
Here's what I end up with when I try a similar test:
----------------------------------------------------------------------------------------
<?xml version="1.0" encoding="iso-8859-1"?>
<!--Created by SBuilderX on 9/12/2014 1:18:45 PM-->
<FSData
version="9.0" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="bglcomp.xsd">
<!--FSX library objects-->
<!--FSX Windsock objects-->
<!--FSX Effect objects-->
<!--FSX Model objects-->
<!--MDL_Model_object_Obj_1-->
<SceneryObject
lat="46.625889"
lon="1.0859467"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<ModelData
sourceFile="..\..\Mdls\Autogenerated_ {63B7343A-B854-44CF-ABEB-1E45D9D23C1C}.mdl" />
<!--MDL_Model_object_Obj_2-->
<SceneryObject
lat="46.625748176548"
lon="1.08619861657232"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<ModelData
sourceFile="..\..\Mdls\Autogenerated_ {63B7343A-B854-44CF-ABEB-1E45D9D23C1C}.mdl" />
<!--MDL_Model_object_Obj_3-->
<SceneryObject
lat="46.6256140660972"
lon="1.08645638638263"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<ModelData
sourceFile="..\..\Mdls\Autogenerated_ {63B7343A-B854-44CF-ABEB-1E45D9D23C1C}.mdl" />
<!--FSX Beacon objects-->
<!--FSX General Buildings-->
</FSData>
----------------------------------------------------------------------------------------
If I remove all but one of the <ModelData /> entries and drop the XML on bglcomp it compiles OK.
----------------------------------------------------------------------------------------
<?xml version="1.0" encoding="iso-8859-1"?>
<!--Created by SBuilderX on 9/12/2014 1:18:45 PM-->
<FSData
version="9.0" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="bglcomp.xsd">
<!--FSX library objects-->
<!--FSX Windsock objects-->
<!--FSX Effect objects-->
<!--FSX Model objects-->
<!--MDL_Model_object_Obj_1-->
<SceneryObject
lat="46.625889"
lon="1.0859467"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<!--MDL_Model_object_Obj_2-->
<SceneryObject
lat="46.625748176548"
lon="1.08619861657232"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<!--MDL_Model_object_Obj_3-->
<SceneryObject
lat="46.6256140660972"
lon="1.08645638638263"
alt="0"
altitudeIsAgl="TRUE"
pitch="0"
bank="0"
heading="0"
imageComplexity="NORMAL">
<LibraryObject
name="{63b7343a-b854-44cf-abeb-1e45d9d23c1c}"
scale="1" />
</SceneryObject>
<ModelData
sourceFile="..\..\Mdls\Autogenerated_ {63B7343A-B854-44CF-ABEB-1E45D9D23C1C}.mdl" />
<!--FSX Beacon objects-->
<!--FSX General Buildings-->
</FSData>
----------------------------------------------------------------------------------------
I will log this issue over at the SBuilderX forum and maybe Luis can look into it when he returns from his sailing expedition

.
Jim