AN ACR FLC FLYING B737-700 FROM EWR FAILS TO PROPERLY LOAD THEIR FLT PLAN AS CLRED BY ATC INTO THEIR FMC RESULTING IN A TRACK DEV.

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THIS MAY BE 2 PROBS. WE DEPARTED THE GATE IN NEWARK JUST BEFORE A TSTM SHUT DOWN THE ARPT. AFTER THE ARPT OPENED BACK UP WE WERE TOLD TO TAXI TO RWY 4L. APCHING THIS POINT WE WERE TOLD TO PULL OVER TO THE R AND CONTACT CLRNC FOR A NEW RTE. CLRNC TOLD US TO STANDBY. AFTER SEVERAL ACFT BEHIND US PASSED US AND WE KNEW THEY WERE GOING THE SAME WAY WE WERE; WE ASKED CLRNC WHERE OUR CLRNC WAS. WE WERE TOLD THEY HAD NO PAPERWORK ON US. WE CALLED OUR COMPANY TO REFILE. SHORTLY THEREAFTER WE WERE CLRED TO THE RWY AND CLRED FOR TKOF. WHY THE BIG DELAY? AS WE WERE TAKING THE RWY FOR TKOF A RTE DOWNLOAD APPEARED ON THE FMC. WE LOADED AND TOOK OFF. WE WERE FILED BIGGY-J75-GVE-CAE. I DON'T KNOW WHERE; BUT GVE DROPPED OUT OF THE RTE AND WE WERE GOING DIRECT TO CAE. CTR ASKED WHAT OUR RTE WAS AND WE RESPONDED AND DISCOVERED WHAT THEY ALREADY KNEW; WE WERE OFF COURSE. I DO NOT KNOW IF THE UPLOAD WAS WRONG AS WE HAD NO TIME TO CHK THIS OR IF WE MISTAKENLY DROPPED IT AS WE WERE DODGING CLOUDS AND STORMS. GUESS I WILL HAVE TO MONITOR RTE MORE CLOSELY AS A FLT PROGRESSES.