While most CodonCode Aligner users never see this problem, the same problem has been reported for many other macOS applications (where it also affected only a small subset of users). It appears to be caused by several bugs in different macOS versions related to window placement, window activation, multiple monitor support, and other issues. This post describes a number of workarounds that have fixed the problems for some users.
1. Switch to another application and then back
Some users reported that the Save dialog was hidden by other windows, and became visible by switching to a different application, and then back to the original application (CodonCode Aligner here). You can switch between applications by using the Dock, or the Command-Tab keyboard shortcut, or by clicking on a window in other application.
The root cause here is a windows activation bug which has been present in form since the earliest versions of Mac OS X.
2. Quit CodonCode Aligner and try again.
Users who experienced this problem with other applications reported that quitting the application and reopening it solved the problem.
3. Eliminate potential problems with network disks
Network disks and related software like Microsoft OneDrive can cause various problems with file dialogs, for example long delays or missing dialogs when network servers become unavailable. To eliminate such problems, eject all mounted network disks; disable iCloud; and disable file sharing software like OneDrive, DropBox, and others. If this fixes the problem, re-enable the apps and services again one by one to find the specific cause.
4. Quit other applications and restart the computer
Some versions of macOS experience multiple problems when many applications are open, and memory use is high. This sometimes caused windows to not draw correctly (appear mostly empty), or new windows to not open at all. The workaround is to quit all open applications, and then restart the computer before re-opening CodonCode Aligner and trying again.
Please note that if you only restart the computer, but have it set to re-open any open applications, the problem may persist.
4. Multiple monitors and older macOS versions
On macOS 12, users of various applications reported problems with missing dialogs when they used multiple monitors (including laptops and external monitors). This problem was at least partly fixed with updates to macOS 12. One workaround was to use the Mac monitor as the primary display. A better solution may be to upgrade to a newer macOS version, if your computer is compatible with a newer version.
5. Disable anti-virus and "helper" software
This is the most common suggestion when reporting problems on Apple discussion forums. While third-party software like anti-virus software can indeed cause some problems, we have not found any reports that third-party software caused the "missing Save dialog" problem. Nevertheless, this might be something worth trying if the workarounds above fail.
If you suspect that third-party software may be a cause of problems, start by booting into safe mode. If this fixes the problem, try to disable extensions and similar software one-by-one to find the actual cause. Note, however, that this approach may be quite tedious, especially if you see the "missing Save dialog" problem only occasionally.
6. Use alternate file dialogs (requires CodonCode Aligner 12.0.4 or newer)
In version 12.0.4 of CodonCode Aligner, we added an option to use alternate file dialogs for exporting, opening, and saving files. The alternate file dialog does not experience the same problems that the usual ("native") file dialog sometimes has, but it also does not have features like the favorite bar or different view options. To use the alternate file dialog in CodonCode Aligner 12.0.4 or newer:
- Start CodonCode Aligner
- Open the settings dialog
- Select the "Open & save" panel
- Check the box "Use alternate file dialog"
- Click the "OK" button