I have checked the code and ADE will look for and copy bglcomp.exe each time it starts in FSX mode. I had thought perhaps it would not copy if the file was already present in the FSX sub folder however that is not the case.
ADE will look first in the path set in Settings > Options > Folders tab for the BglCompiler and if that does not contain the compiler then it will look in the registry entry for the SDK for FSX. If it does not find a compiler in either place it will report an error. So the bglcomp.exe in the FSX sub folder should relate to the SDK specified here:
At the time we designed this there was no FSX:SE and P3D was probably only in v1 or v2, but there is nothing to stop the user from pointing ADE for FSX at any SDK they choose.
Please note that it is only bglcomp.exe which gets copied from the SDK. the schema file bglcomp.xsd is not copied. This is in the FSX sub folder and is based on the schema for the FSX SDK SP2.
Thus if the user specifies an SDK to use with ADE in FSX mode that is later than P3D v1.4 then a mismatch of schema and compiler could arise. This mismatch could result in either the compile failing or the compiled bgl file causing a CTD in FSX. This would happen if the compiler used generated content in the bgl file which FSX can't handle.
Thus while using a compiler from P3D v2 or later may well work in some cases it might well depend on what is in the project file so work for some projects and not others.
The bottom line is that FSX:SE users should either use the FSX (paid for) SDK and compilers or those from the P3D v1.4 SDK.
I realise this may not be relevant to the OP issue here but working with the expected compilers and SDK should eliminate some routes for error or unexpected results.