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Check your .err file

Jim Dirkes' advice to check your .err file to make sure you spelled all the output variables correctly is probably the best first step. If you have already done that, it may be a setting in the software that processes the ESO file into the CSV file that is used by EP-Launch or with the EnergyPlus command line. The software that converts the ESO to CSV is called ReadVarsESO. Read below for options depending on what you do.

EP-Launch

If you are using EP-Launch to simulate the file you can enable more than 255 columns by doing the following. First, select the Options menu item under the View Menu.

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Then under "Miscellaneous" select "Allow More Than 250 Columns"

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The next time you run the simulation you should have as many columns as you want.

Batch File

If you are using the RunEPlus.bat file the %maxcol% parameter needs to be set to "nolimit"

EnergyPlus Command Line

If you are running EnergyPlus using the command line, using the "-r" or "--readvars" option, it should already be producing more than 255 columns.

OutputControl:Files

If you are using in your IDF file, the OutputControl:Files option with the first field for CSV as yes, then it should already be producing more than 255 columns (remember don't use the "-r" or "--readvars" command line option if you do this). Unless you are also showing yes in the third field that controls creating the ESO file, you are probably not using OutputControl:Files.