Well just updated to the latest Beta release, 2.2.0-b18, and that seemed to have done the trick.
Ran the script again and no errors so far…
INFO CoreConsole[2014-04-09 20:22:33] [a2fcb] ---------------------------
INFO CoreConsole[2014-04-09 20:22:33] [a2fcb] INIT
INFO CoreConsole[2014-04-09 20:22:33] [a2fcb] Piwik is installed at: http://[domain]/piwik/index.php
INFO CoreConsole[2014-04-09 20:22:33] [a2fcb] Running Piwik 2.2.0-b18 as Super User: admin
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] ---------------------------
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] NOTES
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] - If you execute this script at least once per hour (or more often) in a crontab, you may disable 'Browser trigger archiving' in Piwik UI > Settings > General Settings.
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] See the doc at: http://piwik.org/docs/setup-auto-archiving/
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] - Reports for today will be processed at most every 10 seconds. You can change this value in Piwik UI > Settings > General Settings.
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] - Reports for the current week/month/year will be refreshed at most every 3600 seconds.
INFO CoreConsole[2014-04-09 20:22:44] [a2fcb] - Archiving was last executed without error 21 days 3 hours ago
INFO CoreConsole[2014-04-09 20:22:45] [a2fcb] - Will process 2 websites with new visits since 21 days 3 hours , IDs: 2, 3
INFO CoreConsole[2014-04-09 20:22:45] [a2fcb] - Will process 2 other websites because some old data reports have been invalidated (eg. using the Log Import script) , IDs: 3, 2
INFO CoreConsole[2014-04-09 18:22:45] [a2fcb] ---------------------------
INFO CoreConsole[2014-04-09 18:22:45] [a2fcb] START
INFO CoreConsole[2014-04-09 18:22:45] [a2fcb] Starting Piwik reports archiving...
INFO CoreConsole[2014-04-09 18:22:58] [a2fcb] Archived website id = 2, period = day, 2255 visits in last 52 days, 1 visits today, Time elapsed: 13.178s
INFO CoreConsole[2014-04-09 18:24:44] [a2fcb] Archived website id = 2, period = week, 6155 visits in last 23 weeks, 42 visits this week, Time elapsed: 105.996s
INFO CoreConsole[2014-04-09 18:25:19] [a2fcb] Archived website id = 2, period = month, 6986 visits in last 23 months, 355 visits this month, Time elapsed: 35.159s
INFO CoreConsole[2014-04-09 18:25:43] [a2fcb] Archived website id = 2, period = year, 6986 visits in last 7 years, 4091 visits this year, Time elapsed: 23.709s
INFO CoreConsole[2014-04-09 18:25:43] [a2fcb] Archived website id = 2, 4 API requests, Time elapsed: 178.105s [1/2 done]
INFO CoreConsole[2014-04-09 18:26:52] [a2fcb] Archived website id = 3, period = day, 2256 visits in last 52 days, 1 visits today, Time elapsed: 69.156s
INFO CoreConsole[2014-04-09 18:28:38] [a2fcb] Archived website id = 3, period = week, 6147 visits in last 23 weeks, 42 visits this week, Time elapsed: 106.241s
INFO CoreConsole[2014-04-09 18:29:08] [a2fcb] Archived website id = 3, period = month, 6978 visits in last 23 months, 355 visits this month, Time elapsed: 29.202s
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Archived website id = 3, period = year, 6978 visits in last 7 years, 4089 visits this year, Time elapsed: 26.367s
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Archived website id = 3, 4 API requests, Time elapsed: 231.127s [2/2 done]
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Done archiving!
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] ---------------------------
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] SUMMARY
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Total visits for today across archived websites: 2
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Archived today's reports for 2 websites
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Archived week/month/year for 2 websites
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Skipped 0 websites: no new visit since the last script execution
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Skipped 0 websites day archiving: existing daily reports are less than 10 seconds old
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Skipped 0 websites week/month/year archiving: existing periods reports are less than 3600 seconds old
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Total API requests: 8
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] done: 2/2 100%, 2 vtoday, 2 wtoday, 2 wperiods, 8 req, 409292 ms, no error
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Time elapsed: 409.293s
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] ---------------------------
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] SCHEDULED TASKS
INFO CoreConsole[2014-04-09 18:29:34] [a2fcb] Starting Scheduled tasks...
task,output
CoreAdminHome.purgeOutdatedArchives,Time elapsed: 0.430s
PrivacyManager.deleteReportData,Time elapsed: 0.041s
PrivacyManager.deleteLogData,Time elapsed: 0.002s
Piwik\Plugins\CorePluginsAdmin\MarketplaceApiClient.clearAllCacheEntries,Time elapsed: 0.114s
CoreAdminHome.optimizeArchiveTable,Time elapsed: 0.822s
INFO CoreConsole[2014-04-09 18:29:43] [a2fcb] done
INFO CoreConsole[2014-04-09 18:29:43] [a2fcb] ---------------------------
DiskStation>