Hello,
Very interesting this, as both I and a friend of mine have had similar experiences with PTSB (having recently moved from Danske Bank, where there was never an issue with tranfers coming in on time, they always went through overnight soon after the particular due date had begun).
PTSB ultimately blamed SEPA for the delay in salaries (from two large, different employers in the case of myself and my friend) not being received until very late on the day they were due in... while colleagues in both of our employers organisations with various other banks, received their salaries first thing the morning they were due without difficulty. On this basis, I cannot help but suspect this is an issue at PTSB's end and not a general SEPA issue.