This is a top of the line web server, running RAID SSDs, 32 GB of RAM, 2.5 GHz Xeon processor, etc.. Every non-JoomDoc page or website runs quickly. On JoomDoc pages it doesn't matter the size of the file referenced, it will take over a minute just to load the page listing the files.

Application 0.000 seconds (+0.000); 1.21 MB (+1.207) - afterLoad
Application 0.097 seconds (+0.097); 10.82 MB (+9.614) - afterInitialise
Application 0.120 seconds (+0.023); 12.42 MB (+1.603) - afterRoute
Application 57.590 seconds (+57.470); 16.87 MB (+4.441) - afterDispatch
Application 57.594 seconds (+0.004); 17.18 MB (+0.317) - beforeRenderModule mod_menu (Operations Links)
Application 57.599 seconds (+0.005); 17.32 MB (+0.142) - afterRenderModule mod_menu (Operations Links)
Application 57.599 seconds (+0.000); 17.32 MB (-0.007) - beforeRenderModule mod_menu (Most Relevant Links)
Application 57.605 seconds (+0.006); 17.35 MB (+0.031) - afterRenderModule mod_menu (Most Relevant Links)
Application 57.606 seconds (+0.000); 17.35 MB (-0.004) - beforeRenderModule mod_joomdoc_explorer (Document Tree)
Application 61.355 seconds (+3.749); 25.45 MB (+8.101) - afterRenderModule mod_joomdoc_explorer (Document Tree)
Application 61.366 seconds (+0.011); 18.52 MB (-6.925) - beforeRenderModule mod_joomdoc_search (Document Search)
Application 61.370 seconds (+0.005); 18.55 MB (+0.030) - afterRenderModule mod_joomdoc_search (Document Search)
Application 61.371 seconds (+0.001); 18.55 MB (-0.002) - beforeRenderModule mod_menu (Main Menu)
Application 61.446 seconds (+0.074); 18.73 MB (+0.179) - afterRenderModule mod_menu (Main Menu)
Application 61.447 seconds (+0.001); 18.72 MB (-0.007) - beforeRenderModule mod_menu (Settings Menu)
Application 61.455 seconds (+0.008); 18.74 MB (+0.018) - afterRenderModule mod_menu (Settings Menu)
Application 61.455 seconds (+0.001); 18.73 MB (-0.007) - beforeRenderModule mod_menu (External Links Menu)
Application 61.468 seconds (+0.013); 18.77 MB (+0.034) - afterRenderModule mod_menu (External Links Menu)
Application 61.469 seconds (+0.001); 18.76 MB (-0.002) - beforeRenderModule mod_search (Smart Search)
Application 61.473 seconds (+0.004); 18.79 MB (+0.024) - afterRenderModule mod_search (Smart Search)
Application 61.474 seconds (+0.001); 18.78 MB (-0.005) - beforeRenderModule mod_custom (Mobile Menu Button)
Application 61.477 seconds (+0.003); 18.80 MB (+0.015) - afterRenderModule mod_custom (Mobile Menu Button)
Application 61.478 seconds (+0.001); 18.79 MB (-0.004) - beforeRenderModule mod_custom (Mobile Search Icon)
Application 61.478 seconds (+0.001); 18.80 MB (+0.005) - afterRenderModule mod_custom (Mobile Search Icon)
Application 61.479 seconds (+0.001); 18.80 MB (-0.002) - beforeRenderModule mod_menu (BaseCamp Logo Menu)
Application 61.483 seconds (+0.004); 18.81 MB (+0.009) - afterRenderModule mod_menu (BaseCamp Logo Menu)
Application 61.483 seconds (+0.001); 18.80 MB (-0.008) - beforeRenderModule mod_custom (BaseCamp Central Subtitle)
Application 61.484 seconds (+0.001); 18.80 MB (+0.005) - afterRenderModule mod_custom (BaseCamp Central Subtitle)
Application 61.489 seconds (+0.005); 18.98 MB (+0.176) - afterRender

There are almost a thousand lines of SQL, I've ran some of the nastier looking ones (lots of joins/left joins) directly into my database and they only take about .043 s to complete.

So has anyone seen this before or suspect what the issue is? Also is there any way to modify these massive SQL statements?

Thanks