Thank you for your response Chris, and apologies for the late reply, I just saw this. I checked the scanner protocol pdf (Siemens Magnotom Prisma_Fit) and  acquisitions were done without motion correction, so that is not the issue and my dcm2niix version is same as above. I ended up using Horos to separate the echoes and then the brik_head AFNI method to prep my dataset for ME-ICA. I am going to give it a try one more time as I want the data to be available publicly in BIDS format, but in the meantime if you came up with a solution, I would appreciate if you could share it here. thank you again!