TagEditor files have to be treated cautiously as they tend to be really sensitive and error-prone. To recognize issues as they arise, it is generally recommended to run the command File > Save Target As ... during translation as often as possible, min. twice per hour. This option generates a clean target file from the current state of the translation and helps you to control from the very beginning, that the hitherto existing translation is technically correct and may be cleaned up without further ado.
Alongside, you should
try to avoid at least 3 of the most common reasons for cleanup failure:
1) Incorrect workstation or folder
A TTX file cannot be processed on different instances of TagEditor/Workbench. The target file must be generated on the same computer, where the translation was done. Furthermore, the source file that was used to create the bilingual TTX file must be located in the same folder as the translated TTX file.
2) Inadmissible segmentation or tag changes
TagEditor files react extremely sensitive on any changes to tags or segmentation. Popular mistakes include generating empty segments, taking over wrong tags from fuzzy matches or eliminating characters between opening and closing tags.
To avoid such mistakes, set the tag verification of TagEditor to the strictest level prior to translation start. (To do so, activate Tools >Options >Verification >Strict, and deactivate Don't check tags when Translating to Fuzzy).
Upon completion of the translation, the verification itself should be executed and any results indicating errors should be corrected (Tools >Verification).
Tag differences can be eliminated by copying the source tag into the translation. Most empty segments or empty opening/closing tags can be fixed by simply adding a space.
3) Special case INX
Trados is equipped with a special filter for INX files only starting from version 7.1. TagEditor, though, can open and process INX files already starting from version 7.0. However, due to the lack of the appropriate filter, these earlier versions cannot generate target files in INX format. There is no workaround - do not edit INX files with Trados versions older than 7.1!