Thank you both for your response I was getting the following warnings when concatenating the runs- where the task in run1 is "step" and the task in run2 is "stand".

++ Wrote matrix values to file X.nocensor.xmat.1D
++ ----- Signal+Baseline matrix condition [X] (1278x155): 3.58672 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=1.99236
* 2 singular values are less than cutoff=1.99236e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
0 2.99845e-08 0.154872 0.252929 0.267126
0.269645 0.283077 0.29791 0.316453 0.330186
0.341668 0.342179 0.349798 0.36136 0.376046
0.384083 0.390261 0.392637 0.398798 0.406672
0.416771 0.436802 0.447039 0.450877 0.460095
0.468965 0.47245 0.482391 0.488204 0.488812
0.502547 0.524036 0.532249 0.549107 0.551849
0.554817 0.563324 0.582939 0.59116 0.591652
0.602114 0.602379 0.605666 0.60847 0.61215
0.614238 0.615671 0.624534 0.656948 0.663289
0.669554 0.672267 0.684408 0.687056 0.698804
0.718081 0.727385 0.734869 0.743858 0.760883
0.761613 0.764951 0.767428 0.770707 0.77948
0.782271 0.788038 0.817865 0.835145 0.843293
0.844543 0.854562 0.857737 0.858406 0.869383
0.879436 0.893794 0.897641 0.899713 0.916866
0.928522 0.945479 0.955541 0.958643 0.973911
0.977395 0.977843 0.991498 1.004 1.00762
1.00825 1.01852 1.01985 1.03094 1.03686
1.03754 1.04878 1.05049 1.05411 1.06561
1.06978 1.08776 1.10565 1.10678 1.11304
1.11314 1.11315 1.11781 1.1338 1.15188
1.15495 1.16197 1.17808 1.18682 1.23882
1.24677 1.24769 1.24847 1.25219 1.26929
1.27469 1.27684 1.29279 1.2955 1.29881
1.31165 1.33317 1.33667 1.34196 1.34841
1.35985 1.36439 1.37349 1.38997 1.40454
1.42434 1.44648 1.44826 1.45726 1.45848
1.4711 1.48664 1.51152 1.52194 1.5451
1.55 1.55583 1.57761 1.6568 1.67749
1.70381 1.71769 1.7346 1.7999 1.99236
++ ----- Signal-only matrix condition [X] (1278x11): 1.18921 ++ VERY GOOD ++
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=1.41421
* 2 singular values are less than cutoff=1.41421e-07
* Implies strong collinearity in the matrix columns!
++ Signal-only matrix singular values:
0 0 1 1 1
1 1 1 1 1.41421
1.41421
++ ----- Baseline-only matrix condition [X] (1278x144): 3.57446 ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (1278x108): 2.65822 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (1278x36): 1.01608 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 0.000457856 ++ OK ++
++ Matrix setup time = 22.29 s

Warnings regarding Correlation Matrix: X.xmat.1D

severity correlation cosine regressor pair
-------- ----------- ------ ----------------------------------------
high: 0.705 0.725 (16 vs. 41) Run#1Pol#0 vs. step15_on#0
high: 0.705 0.725 (12 vs. 40) Run#2Pol#0 vs. stand30_on#0