FAQ: What are some of the possible explanations for an inability to clone an insert into a pMAL vector?

The most common explanation for this is technical difficulties with the subcloning. Another explanation is that expression of the fusion is toxic to E. coli. The tac promoter induction ratio on the pMAL plasmids is about 1:30, so if the induced level of the fusion is 40% of the total cellular protein, the uninduced level works out to over 1%. This amount of a protein can be toxic, either because of its function (e.g., a protease) or because of its general properties (e.g., very hydrophobic).
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