Hi Sid,
Did you start a new career when updating to v1.3
Have you added the patch for the ships
The only change in v1.3 was adjusting boat types (I checked all layers to ensure none were missed) and reducing and fixing scapa
Run TDWs SH5 valaidtor to check campaign files etc
The missing harbour walls are from a mem issue. (this could also be the ctds cause)
Are you using a 32bit OS - if so you may need to apply the 3gig switch.