Logistic regression model returns lower than expected logit

#1
Hi all,
I'm using a logistic regression model with 3 variables to separate true positives from errors in a data set. All in all it seems to perform quite well, but for some reason the logit values seem to be much lower that they should be. What I mean is that in order to get ~90% sensitivity and ~90% precision I have to set my logit cutoff at around -1 or 0. From my (very limited) understanding a logit cutoff of 0 should give you around 50% precision (half your final data set it TP, half is FP). I get this effect when I run the model on the same data it was trained on. My only idea for a cause of this so far is that my training data set had roughly 10x as many true-negative data points as true-positive data points, but evening them out didn't seem to fix the problem much.

Here is my model with output from R's glm
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Deviance Residuals:
Min 1Q Median 3Q Max
-4.48817 -0.17130 -0.10221 -0.05374 3.36833

Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.85666 0.33868 -2.529 0.011425 *
var1 1.08770 0.15364 7.080 1.45e-12 ***
var2 0.67537 0.08003 8.439 < 2e-16 ***
var3 -1.25332 0.33595 -3.731 0.000191 ***
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Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

Null deviance: 1230.63 on 2034 degrees of freedom
Residual deviance: 341.81 on 2031 degrees of freedom

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thanks in advance!