After investigation, this is the expected behavior.
For instance the problem pBop contains 31212 variables. The problem can be trivially decomposed into 25054 independent sub-problems, all but one containing only one variable.
The current heuristic is to split the time limit proportionally to the number of variables of a sub-problem. That means that all one-variable sub-problems are given 2ms to solve and the large one 12 seconds. The one-variable sub-problems are obviously super fast to solve, hence the total solving time of 13 seconds.
A workaround would be to not introduce all those one-variable sub-problems.
Hope it helps.