I have not seen this problem before, it might be worth submitting a request on SupportNet.
Are you referring to the existing custom component in the drawing? If this is the case then it probably that you have the 'Convert to Block' selected in the 'Objects' area of the 'Write Block' dialog. When creating a block you have the choice of what you want to do with the original source entities, you can:
Retain = Leaves the custom component or any selected entities as they are
Convert to Block = Converts all of the custom components or entities selected into a block
Delete from Drawing = This may come as a surprise but...it deletes them from the drawing.
If this answers your question please mark it as 'Answered', if not let me know and I'll see if I can answer it