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The client software was updated many times in the late 1990s. Version 1.49 was final for Windows 3.1, except for a date problem that was fixed in version 1.51. Versions 4.0.11 and 5.0.33 were final for Windows 95 and later. Version 4 had attachments and a spell checker, and displayed fonts and colors. For old messages, it had storage folders, each stored in a separate file containing up to 1000 messages.
Version 5 added an ineffective integral twit/spam filter and the ability to write messages in chosen fonts and colors with inline images. It stored its old messages in a different format, with one large file for all messages. When disk free space was not several times larger than the message file, it often suffered "folder collapse" in which all messages returned to the "Inbox" or disappeared.
As of December 1, 2004, use of an e-mail client such as the Juno client, Microsoft Outlook Express, or Eudora had ceased to be free. Users who wished to use an e-mail client instead of Juno's web-based e-mail interface were required to pay for either Juno Platinum or Juno Megamail.
The Juno client software's version 5.0, build 33, would not work with Internet Explorer 7. However, by the time Microsoft released the final version of IE7, Juno had released Juno 5.0 build 49, which resolved the issues with IE7 and made it compatible with Windows Vista.
Version 8, compatible with Windows 7, was released in 2009. The proprietary mailers were only slightly supported in the 21st century, and users were expected to use POP3 standard mail clients.
No version of Juno's offline mail reader was made to use third party utilities to scan for viruses or clean out E-mail spam among messages that had already been downloaded. Versions 5 and 8 could weed downloaded email messages individually by exact email address matches; however, there were no wildcards, boolean exclusion-filters, or routing features to facilitate this. The company opened a spamdesk to help screen spam at the servers, thus minimizing the amount of spam received by the Juno client.
While the Juno client software could back up e-mails and addresses, it did not support exporting these to other clients, nor did other clients support importing from Juno. Only a handful of third-party utilities were made that could do anything with the proprietary message storage format; instead, users were forced to use third party applications to convert and export the data, principally juno5bdb for messages (which Juno stored in a Berkeley DB), and Dawn for addresses