One way to get what you wanted is to run PROC MIXED twice. Once with the (ref="1") option in the CLASS statement so you get what you want for the parameter estimates, and no STORE statement is needed. Then you can run PROC MIXED the second time, with no (ref="1") option in the CLASS statement. Use the STORE statement this time. Then your PROC PLM output should display the time in the order as you wanted. To speed up the second PROC MIXED, you might add NOTEST option in the MODEL statement, also add NOINFO NOITPRINT NOCLPRINT options in the PROC MIXED statement.
Alternatively, you might define a format for your variable time_dichotomous_number, such that the format for "1" comes first alphabetically, and assign this format to the variable time_dichotomous_number.
Yes, the values being plotted are the predicated values from your PROC MIXED model.
Hope this helps,
Jill
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