Sounds like Air Malta were justified in denying boarding since you were late for check-in. I appreciate that it may not be your fault but that is irrelevant to them.
Such unfortunate situation highlights once again the risks of buying (as I assume) separate tickets for a multiple legs journey. If anything happens with the 1st flight to the connecting point, you are on your own. The initial carrier will claim that it fulfilled its contract by transporting you ''within reasonable delay'' to your destination whilst the 2nd carrier will claim that you did not comply with its instructions with regard to check-in deadlines. In this case, it's even worse since neither airlines can be blamed for what looks like a failure on the part of baggage handlers likely to be employed by the airport authorities.
A lesson to be learned...
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