I created a flight plan a couple days ago for KSAN to KLAX. It files fine. Today I'm actually finally going to fly the route, but the departure direction is changed at KSAN. So I've started a new flight plan from runway 09 instead of 27. Now the flight plan won't file. I see an error in the Pilot2ATC log file:

Begin FPLFile 12/25/2018 22:17:46
AssignedSID: RW09-FALCC1-SLI - 
AssignedRunway: RW09 - 
FltPlan ActiveSID: RW09-FALCC1-SLI - 
Error in btnFPLFile: System.ArgumentOutOfRangeException: Non-negative number required.
Parameter name: count
   at System.ThrowHelper.ThrowArgumentOutOfRangeException(ExceptionArgument argument, ExceptionResource resource)
   at System.Collections.Generic.List`1.RemoveRange(Int32 index, Int32 count)
   at P2A_2018.FltPlan.CalculateDescent(FPWpt StartWpt, Int32 StartAlt, FPWpt EndWpt, Int32 ActualGndSpeed)
   at P2A_2018.FltPlan.CalculateTODDescent(Int32 ActualGndSpeed)
   at P2A_2018.FltPlan.Validate(Boolean CalcTOD, Int32 AcftGS, Boolean SuppressBuildRte)
   at P2A_2018.FltPlan.FileFltPlan()
   at P2A_2018.ucFltPln.n.a()
FltPlan ActiveAPPR: ILS - RW25R - I25R - 
FltPlan ActiveAPPR: ILS - RW25R - I25R - 
ucFltPln ValidateCurrentFltPlan Started
ucFltPln ValidateCurrentFltPlan Done

Here's a link to relevant files:

https://drive.google.com/drive/folders/1rE0qMnjQkAzToHkuz2GlSUTW4dyTCnvh?usp=sharing

Updated link: https://drive.google.com/drive/folders/1jNjJqaCXCI8SZN61AyfTzaxahRwO0u39?usp=sharing

I tried loading your plan and I didn't try to file but did try to validate.

At first it wasn't even showing in the map.  I went into SID and just set the same information I saw before and loaded it.

This gave me an error about TOD calculation.  

I changed the ground speed to 120 and now the plan gets past validate.

I have my p2atc flight plan config for all help from ATC disabled and Force pilot runway enabled so it doesn't mess with your plan.  I then use autoplan which kind of checks your plan and I got the TOD calculation error.

You didn't give any information on how you changed the runway to rw09.