I recognize this issue. I am affected by it too, but in my case I see it when I run my program from the Wolfram Script environment (I am not using webMathematica). Under 10.2 I always see the issue when running scripts, but under 10.3 the issue is not preset if the front end is not open.

I can run my script with my Mathematica Front End closed, but I don't think you can do that with webMathematica. I have contacted support and they have reproduced the problem [CASE:3450946].

My script runs automatically everyday in order to generate and email a report. Unfortunately I keep forgetting to close my Mathematica Front End and therefore my report is sometimes missing the ticks. I really would like to have a workaround this issue.