Maybe it is about system cleaning. When we change column we must clean all system. If you forget it and then you begin different mobile phase it may be a big problem :(

Especially after using salty mobile phase must be carefull. For ex. ıf the problem is in the DAD entery dismantle the screw with pliers need to inject a syringe of ultrapure water.

https://www.chem.agilent.com/Library/slidepresentation/Public/Tips_and_Tricks_HPLC_Troubleshooting.pdf

http://chem-fuuast.weebly.com/uploads/1/2/8/9/12894433/shimadzu_hplc_standard_operation_procedure_by_dr._sana_mustafa.pdf

http://www.proteinsandproteomics.org/content/free/protocols_1/pro04-b.html

http://www.science.uva.nl/research/its/research/pa/docs/docs/voorkomen_beter_dan_genezen.pdf

Can  you please tell me what type of sample you are injecting in the system? The 1100 series system have no internal needle wash mechanism so it gets choked after some injections, its also depend up on type of sample matrix you are injecting. Use needle wash option and inject 5-10 injections of Methnol/water or Acetonitrile/water and wash system with 50:50 methanol/water, it will clean needle seat & tubing. May be this will work, it is related to cleaning of your needle seat and tubing.

I injecting 5uL of plasma extract after protein precipitation and double centrifugation and injecting the supernatant.

I have tried your suggestions of washing with 50:50 methanol/water but now the main problem now is that in the normal mainpass mode the flow is splitting such that most of the flow is coming through the metering device into the needle and goes into the needle seat. There is very little going to the column through port 6.

This should be very easy to diagnose. Two probable reasons for your problem: (1) You are clogging the HPLC injector because you are not filtering your samples (0.45u); (2) Your rotor seal is scratched and/or worn resulting in cross flow across ports.

First of all, replace the rotor seal with a new one. These are consumable parts and they do not last long. They are inexpensive and designed to be replaced on a regular basis (a PM item). Dirty samples or buffered mobile phases will wear them out quickly. Clean the valve interior and check the stator and isolation seals (behind the rotor seal) for contamination, salt crystals and/or ground up plastic (rather common). Clean everything. Replace all parts which are worn or contaminated. Once that is done, do NOT try to backflush the injector. There is no need for this and this is a "flow through" injection system designed to keep itself very clean (if maintained). Liquid is supposed to flow through the metering pump, needle and needle seat during normal operation (that is the flow path). Fluid enters port #1 and exits to the column at port #6. If high pressure is detected and the system is shutting down you probably have a worn rotor seal which is re-routing liquid to the wrong places  OR the needle seat is clogged. The needle seat is another one of those consumable parts designed to be replaced on a regular basis like the rotor seal. Since a newly aspirated sample's first contact with the HPLC is the narrow needle seat, this is where a clog is most likely to occur. The cure is: (1) Replace the needle seat; (2) Filter all samples before placing in the HPLC; (3) Always be aware of conditions where the injection solution could cause something to crystallize or fall out of solution when it hits the mobile phase causing a clog. Your mobile phase should be the same as your injection solution.

BTW: The previous poster's statement, "The 1100 series system have no internal needle wash mechanism so it gets choked after some injections", is not accurate and implies they are not experienced in using Agilent brand HPLC autosamplers such as the types used in the 1100, 1200, 1260 and 1290-series systems. Users of other brands of HPLC systems (e.g. Waters, Shimadzu, Dionex...) who first start to use an Agilent brand system often make the error of treating it like every other system they have used, when in fact, they are very different in design. Agilent's A/I use a flow-through design which flushes the entire sampler flow path during the run so almost no carryover or washing is possible or needed (this is completely different than how a typical Waters, Shimadzu, Thermo or other brand system works). All of this is explained in the User's Manual. And yes, all Agilent A/S have a built-in provision to use a Wash Vial, if you want to. You simply tell the system where the wash vial is located in the system, or, you can simply program the system to wash the needle any way you want using any available vial with the built-in programing steps. You should not experience clogging or obstructions during injection IF you maintain the A/S (e.g. regular PM's), filter samples, dissolve ALL samples in mobile phase and make sure they are 100% soluble (not 99%) in the solution. These are some of the most reliable and rugged autoinjector systems overall.