Keep Your passport while applying & "Not straightforward" email

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Hi

I am an Indian national who recently applied for UK visit visa (less than six months). However, I availed VFS's "Keep your passport while applying" service by paying extra fee. On 24th May, I received an email from New Delhi High commission stating my application is not "straight forward" and it will take more than the established customer service targets (15 working days). I am on 11th working day now. My question is:

1. Has anyone before availed this service of "Keep your passport while applying"? If yes, what is the experience like? When do they ask you to submit your passport? VFS told me to submit after 10 days and UKVI told me in email to submit once the decision has been made.

2. I have no clue why my application can be "not straight forward". I have previously stayed in UK for a year under ICT visa for a year and left before expiry. After that I went back to UK once for 9-10 days for tourism by applying a visit visa which was granted. I have never had any refusal in any country whatsoever, and been to 40+ country. No NHS debt, no criminal record whatsoever anywhere, extremely well established with a reputed consulting MNC and frequently traveled all over the world. Any idea guys why my application is withheld?