Besides links/visits to Pakistan, I’ve also had colleagues who had their visas take much longer to process than usual (1-6 months) for other links, such as links/visits to Iran, Palestine etc. This is despite them previously having travelled to India and acquiring visas easily. Luck of the draw unfortunately on the first person to process your application and whether they flag it, after which it disappears into a black hole. (I hope you got it in the end.)