Thank you for your feedback and for contacting us with this question!
It really seems that there's something strange happens in this case. Sometimes there might be some strange records (records that do not follow rules from the debug logs format description) in the debug logs and this is why the IDE might fail to reconstruct a whole execution flow correctly. Also, there might be something that the IDE just do not handle properly (however, the number of such cases rapidly is going closer and closer to zero over the time).
May I please ask you to check one thing for this case:
1. when you start debugging your code where the issue, right after a debug starts please navigate to the Main Menu -> Debug -> Show Debug Logs;
2. this will open the panel that will show you debug log entries that were parsed as a part of the previous step;
3. in the case, when debugging starts on a strange part of the code as you describe - what do you see in the Deubg Logs panel?
Do you see there all first 759 lines of log file?
4. if the number of entries shown in the Debug Logs panel is significantly less (compared to the line from what the IDE starts debugging), can you please check the log file and let us know what's located in a couple lines before the lines that you see in the Debug Logs panel?
Additionally, in order for us to resolve the issue, this would be very helpful and we would greatly appreciate if you could share with us your Debug Log file where this issue is reproduced.
In the case, if this is acceptable for you – please ensure that there is no any confidential information or sensitive information (data records, certain classes or method names, SOQL queries which contain some valuable information, etc.). If such information is present in the file, please replace it with some tag, for example, *hidden info*, however, don't remove it at all - the file structure is very important for an ability to analyze the file properly.
Looking forward to your response.