It is most likely a matrix effect. 

You could wash the column with a reasonable concentration of the strong solvent of your mobile phase, with it being higher than at the end of the gradient. Then you should inject the blank again. Also, check to make sure the peak you are getting in the blank is not at the dead volume or solvent front.

If not, then after washing if there is something on the column, it should be gone or greatly reduced in size. If you determine it is something from the matrix, you need to go to a higher concentration of EtOH or IPA at the end of the gradient. This will clean the column better.

If it reappears after a while, then you will probably have to institute a washing step after a certain number of injections.