Maybe I read that wrong, but apples-to-apples (Pew defense to Pew overall population), it looks like 1.7% and 1.7%.
In Table 1 in the link, the "DEOMI" column(1.09%) is from a survey of service members, the DMDC (0.32%) comes from what service members indicate on their paperwork as their religious preference. The remaining two columns (1.17 and 1.7%) are from surveys of civilians, and so indicate the percent of Jews in the civilian population).
The large discrepancy between the two military figures (1.09 versus 0.32) may represent how many people consider themselves ethnically Jewish versus how many consider themselves actually as believing Jews.