Hopefully some of the contributors familiar with the ME Suit will give you some suggestions. In the meantime, what font are you using? Does it happen if you use a different font or if you start a new document? Is it just in one particular document?
it comes and goes with different fonts on different files, sometimes creating outlines help but I just can’t convert every file I make, especially the long ones, it’s time consuming and very annoying...
(1) Exactly what version of InDesign ME are you using?
(2) Give specific examples of fonts with this issue.
(3) Since this is the “ME” version, advise as to whether this is happening with left-to-right text as with Western Latin character set text or with right-to-left text as with Arabic, Hebrew, or Farsi and if the latter, whether any special characters such as Hebrew nikud is used in the text.
(4) I assume you are not seeing the problem on-screen in InDesign. Are you seeing when viewing in Adobe Reader or Acrobat on screen or only when printing? Perhaps you can provide some screen shots.