Online Digital Publication

I publish print magazines using InDesign and up until a couple of years used a company called 3D Issue to roll up my final printer version PDF and create a flip book for access to the current magazine on my website.

When 3DIssue could not explain why for the first time in 10 years the online version had changed the fonts in my print version PDF - I  turned to the Adobe online digital publication and found it worked very well - I simply used the final version from InDesign and changed the dropdown to Digital Publishing and then Publish Online. I then copy and paste the URL on the link on the website. 

This morning I have done that and the digital view PDF has images missing on several pages ( both PDF and JPEG placements). I have tried it again several times using the both the IDML version and the regular version in the Packaged folder

Any suggestions?