Found the culprit:
229 <!-- The default high-performance update handler -->
230 <updateHandler class="solr.DirectUpdateHandler2">
231 <!-- AutoCommit
232
233 Perform a hard commit automatically under certain conditions.
234 Instead of enabling autoCommit, consider using "commitWithin"
235 when adding documents.
236
237 http://wiki.apache.org/solr/UpdateXmlMessages
238
239 maxDocs - Maximum number of documents to add since the last
240 commit before automatically triggering a new commit.
241
242 maxTime - Maximum amount of time in ms that is allowed to pass
243 since a document was added before automaticly
244 triggering a new commit.
245 openSearcher - if false, the commit causes recent index changes
246 to be flushed to stable storage, but does not cause a new
247 searcher to be opened to make those changes visible.
248 -->
249 <autoCommit>
250 <maxTime>15000</maxTime>
251 <openSearcher>false</openSearcher>
252 </autoCommit>
253
254 <!-- softAutoCommit is like autoCommit except it causes a
255 'soft' commit which only ensures that changes are visible
256 but does not ensure that data is synced to disk. This is
257 faster and more near-realtime friendly than a hard commit.
258 -->
259
260 <autoSoftCommit>
261 <maxTime>1000</maxTime>
262 </autoSoftCommit>
commented out the autocommit and autosoftcommit sections and the index doesn't update incrementally any more. Appears this is a new argument added in solr 4. Hopefully this helps someone else in the future.
EDIT: This is located in the SolrConfig/conf/solrconfig.xml file.