In LDMS 9.5 and 9.6 we did change how packages are selected in the Portal. We have made it similar to how you select files in Windows Explorer. If you click a single package at a time it will only highlight one, but if you hold CTRL you can click on as many packages as desired and all will stay highlighted. In your case, it is mistaking your missed check box as a selection of a single package. You can also hold shift to select a range of packages.
Also, I'm not sure if you are using OSD Scripts or Provisioning for your Image deployments but with Provisioning you can automate a large portion of the process so that you do not need to use the portal for each deployment. Another option, if using the portal is un-avoidable and provisioning is not an option, is to deploy the most common packages together in a Bundle reducing the amount of packages you'll need to select in the Portal for deployment.
Please let me know if there are any other questions.
Thank you, you've likely saved both my hair and sanity
Glad to hear it and thanks for the feedback.